Mercurial > repos > davidecangelosi > pipe_t
annotate pipe-t.R @ 2:6cd22b1fbf6d draft
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
author | davidecangelosi |
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date | Mon, 06 May 2019 05:37:40 -0400 |
parents | 185ba61836ab |
children | e2fcf5a4609c |
rev | line source |
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0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
1 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
2 cat("\n Started! \n") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
3 #sessionInfo() |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
4 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
5 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
6 # Send R errors to stderr |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
7 options(show.error.messages = F, error = function(){cat(geterrmessage(), file = stderr()); q("no", 1, F)}) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
8 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
9 # Avoid crashing Galaxy with an UTF8 error on German LC settings |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
10 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
11 suppressPackageStartupMessages({ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
12 library(HTqPCR) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
13 library(base) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
14 library(Biobase) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
15 library(utils) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
16 library(stats) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
17 library(graphics) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
18 library(grDevices) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
19 library(RColorBrewer) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
20 library(limma) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
21 library(RankProd) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
22 library(methods) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
23 library(impute) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
24 library(BBmisc) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
25 library(affy) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
26 library(psych) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
27 #library(gmp) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
28 library(zoo) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
29 library(nondetects) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
30 library(Hmisc) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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31 #library(missForest) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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32 #library(mice) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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33 }) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
34 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
35 cat("\n R libraries...loaded!\n") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
36 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
37 args = commandArgs(trailingOnly=TRUE) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
38 dpfiles<-basename(args[1]) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
39 path000<-dirname(args[1]) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
40 format<-args[2] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
41 nfeatures<-args[3] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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42 rawout<-args[4] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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43 path <- args[5] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
44 dcCtmin<-args[6] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
45 dcCtmax<-args[7] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
46 dcflag<-args[8] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
47 x<-args[9] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
48 normalizationMethod<-args[10] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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49 if (normalizationMethod=="deltaCt") { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
50 normalizers<-args[11] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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51 outputNorm<-args[12] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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52 outputECDF<-args[13] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
53 percentofnastoremove<-args[14] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
54 outputRemaining<-args[15] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
55 imputeMethod<-args[16] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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56 if (imputeMethod=="knn") { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
57 kappa<- args[17] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
58 macsp<-args[18] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
59 outputIMP<-args[19] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
60 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
61 DEAMethod<-args[20] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
62 if (DEAMethod=="ttest") { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
63 alternative<- args[21] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
64 paired<-args[22] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
65 replicates<- args[23] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
66 sort<-args[24] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
67 stringent<- args[25] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
68 padjust<-args[26] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
69 outputDEA<-args[27] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
70 filtnames<-args[28] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
71 } else { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
72 outputDEA<-args[21] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
73 filtnames<-args[22] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
74 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
75 } else { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
76 #mean, median, nondetects, cubic |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
77 outputIMP<-args[17] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
78 DEAMethod<-args[18] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
79 if (DEAMethod=="ttest") { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
80 alternative<- args[19] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
81 paired<-args[20] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
82 replicates<- args[21] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
83 sort<-args[22] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
84 stringent<- args[23] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
85 padjust<-args[24] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
86 outputDEA<-args[25] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
87 filtnames<-args[26] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
88 } else { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
89 outputDEA<-args[19] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
90 filtnames<-args[20] |
185ba61836ab
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91 } |
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92 } |
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93 }else { |
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94 outputNorm<-args[11] |
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95 outputECDF<-args[12] |
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96 percentofnastoremove<-args[13] |
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97 outputRemaining<-args[14] |
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98 imputeMethod<-args[15] |
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99 |
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100 if (imputeMethod=="knn") { |
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101 kappa<- args[16] |
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102 macsp<-args[17] |
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103 outputIMP<-args[18] |
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104 |
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105 DEAMethod<-args[19] |
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106 |
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107 if (DEAMethod=="ttest") { |
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108 alternative<- args[20] |
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109 paired<-args[21] |
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110 replicates<- args[22] |
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111 sort<-args[23] |
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112 stringent<- args[24] |
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113 padjust<-args[25] |
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114 outputDEA<-args[26] |
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115 filtnames<-args[27] |
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116 } else { |
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117 outputDEA<-args[20] |
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118 filtnames<-args[21] |
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119 } |
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120 } else { |
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121 #mean, median, nondetects, cubic |
185ba61836ab
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122 outputIMP<-args[16] |
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123 DEAMethod<-args[17] |
185ba61836ab
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124 if (DEAMethod=="ttest") { |
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125 alternative<- args[18] |
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126 paired<-args[19] |
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127 replicates<- args[20] |
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128 sort<-args[21] |
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129 stringent<- args[22] |
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130 padjust<-args[23] |
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131 outputDEA<-args[24] |
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132 filtnames<-args[25] |
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133 |
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134 } else { |
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135 outputDEA<-args[18] |
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136 filtnames<-args[19] |
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137 |
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138 } |
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139 } |
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140 } |
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141 cat("\n Initialization completed! \n") |
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142 |
2
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143 .readCtEDS <- |
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144 function(readfile=readfile, n.data=n.data, i=i, nspots=nspots, ...) |
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145 { |
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146 # Scan through beginning of file, max 100 lines |
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147 file.header <- readLines(con=readfile, n=100) |
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148 n.header <- grep("^Well", file.header) |
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149 if (length(n.header)==0) |
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150 n.header <- 0 |
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151 # Read data, skip the required lines |
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152 out <- read.delim(file=readfile, header=TRUE, colClasses="character", nrows=nspots*n.data[i], skip=n.header-1, strip.white=TRUE, ...) |
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153 out |
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154 } # .readCtEDS |
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155 |
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156 |
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157 .readCtPlain <- |
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158 function(readfile=readfile, header=header, n.features=n.features, n.data=n.data, i=i, ...) |
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159 { |
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160 # A check for file dimensions. Read a single file. |
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161 sample <- read.delim(file=readfile, header=header, ...) |
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162 nspots <- nrow(sample) |
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163 if (nspots != n.features*n.data[1]) |
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164 warning(paste(n.features, "gene names (rows) expected, got", nspots)) |
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165 # Read in the required file |
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166 out <- read.delim(file=readfile, header=header, colClasses="character", nrows=nspots*n.data[i], ...) |
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167 # Return |
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168 out |
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169 } # .readCtPlain |
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170 |
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171 .readCtSDS <- |
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172 function(readfile=readfile, n.data=n.data, i=i, nspots=nspots, ...) |
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173 { |
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174 # Scan through beginning of file, max 100 lines |
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175 file.header <- readLines(con=readfile, n=100) |
6cd22b1fbf6d
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176 n.header <- grep("^#", file.header) |
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177 if (length(n.header)==0) |
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178 n.header <- 0 |
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179 # Read data, skip the required lines |
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180 out <- read.delim(file=readfile, header=FALSE, colClasses="character", nrows=nspots*n.data[i], skip=n.header, strip.white=TRUE, ...) |
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181 # Return |
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182 out |
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183 } # .readCtSDS |
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184 |
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185 .readCtLightCycler <- |
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186 function(readfile=readfile, n.data=n.data, i=i, nspots=nspots, ...) |
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187 { |
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188 # Read data, skip the required lines |
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189 out <- read.delim(file=readfile, header=TRUE, as.is=TRUE, nrows=nspots*n.data[i], skip=1, strip.white=TRUE, ...) |
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190 # Return |
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191 out |
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192 } # .readCtLightCycler |
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193 |
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194 .readCtCFX <- function(readfile=readfile, n.data=n.data, i=i, nspots=nspots, ...) |
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195 { |
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196 # Read data, skip the required lines |
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197 out <- read.csv(file=readfile, header=TRUE, as.is=TRUE, nrows=nspots*n.data[i], strip.white=TRUE, ...) |
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198 # Return |
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199 out |
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200 } # .readCtCFX |
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201 |
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202 .readCtOpenArray <- |
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203 function(readfile=readfile, n.data=n.data, i=i, nspots=nspots, ...) |
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204 { |
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205 # Read data |
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206 out <- read.csv(file=readfile, header=TRUE, as.is=TRUE, nrows=nspots*n.data[i], strip.white=TRUE, ...) |
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207 # Regard those marked as outliers as "Unreliable" |
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208 out$ThroughHole.Outlier[out$ThroughHole.Outlier=="False"] <- "OK" |
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209 out$ThroughHole.Outlier[out$ThroughHole.Outlier=="True"] <- "Unreliable" |
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210 # Return |
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211 out |
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212 } # .readCtOpenArray |
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213 |
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214 .readCtBioMark <- |
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215 function(readfile=readfile, n.data=n.data, i=i, nspots=nspots, ...) |
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216 { |
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217 # Scan through beginning of file, max 100 lines |
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218 file.header <- readLines(con=readfile, n=100) |
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219 n.header <- grep("^ID", file.header)-1 |
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220 if (length(n.header)==0) |
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221 n.header <- 0 |
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222 # Read data, skip the required lines |
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223 out <- read.csv(file=readfile, header=TRUE, as.is=TRUE, nrows=nspots*n.data[i], skip=n.header, strip.white=TRUE, ...) |
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224 # Convert the calls into flags |
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225 out$Call[out$Call=="Pass"] <- "OK" |
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226 out$Call[out$Call=="Fail"] <- "Undetermined" |
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227 # Return |
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228 out |
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229 } # .readCtBioMark |
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230 |
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231 |
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232 |
0
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233 readCtDataDav<- |
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234 function (files, path = NULL, n.features = 384, format = "plain", |
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235 column.info, flag, feature, type, position, Ct, header = FALSE, |
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236 SDS = FALSE, n.data = 1, samples, na.value = 40, sample.info, |
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237 ...) |
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238 { |
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239 if (missing(files)) |
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240 stop("No input files specified") |
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241 if (length(files) != length(n.data) & length(n.data) != 1) |
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242 stop("n.data must either be a single integer, or same length as number of files") |
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243 if (length(n.data) == 1) |
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244 n.data <- rep(n.data, length(files)) |
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245 nsamples <- sum(n.data) |
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246 ncum <- cumsum(n.data) |
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247 s.names <- NULL |
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248 nspots <- n.features |
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249 if (SDS) { |
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250 warning("Please use format='SDS'. The SDS' parameter is retained for backward compatibility only.") |
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251 format <- "SDS" |
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252 } |
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253 if (!missing(flag) | !missing(feature) | !missing(type) | |
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254 !missing(position) | !missing(Ct)) { |
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255 warning("Please use 'column.info' for providing a list of column numbers containing particular information. The use of 'flag', 'feature', 'type', 'position' and 'Ct' is deprecated and will be removed in future versions.") |
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256 } |
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257 if (missing(column.info)) { |
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258 column.info <- switch(format, EDS = list(flag="EXPFAIL", feature="Target.Name", position="Well.Position", Ct="CT"), |
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259 plain = list(flag = 4, |
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260 feature = 6, type = 7, position = 3, Ct = 8), SDS = list(flag = 4, |
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261 feature = 6, type = 7, position = 3, Ct = 8), LightCycler = list(feature = "Name", |
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262 position = "Pos", Ct = "Cp"), CFX = list(feature = "Content", |
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263 position = "Well", Ct = "Cq.Mean"), OpenArray = list(flag = "ThroughHole.Outlier", |
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264 feature = "Assay.Assay.ID", type = "Assay.Assay.Type", |
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265 position = "ThroughHole.Address", Ct = "ThroughHole.Ct"), |
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266 BioMark = list(flag = "Call", feature = "Name.1", |
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267 position = "ID", Ct = "Value")) |
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268 } |
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269 X <- matrix(0, nspots, nsamples) |
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270 X.flags <- as.data.frame(X) |
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271 X.cat <- data.frame(matrix("OK", ncol = nsamples, nrow = nspots), |
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272 stringsAsFactors = FALSE) |
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273 for (i in seq_along(files)) { |
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274 if (i == 1) { |
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275 cols <- 1:ncum[i] |
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276 } |
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277 else { |
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278 cols <- (ncum[i - 1] + 1):ncum[i] |
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279 } |
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280 readfile <- ifelse(is.null(path), files[i], file.path(path, |
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281 files[i])) |
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282 sample <- switch(format, EDS =.readCtEDS(readfile = readfile, |
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283 n.data = n.data, i = i, nspots = nspots, ...), plain = .readCtPlain(readfile = readfile, |
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284 header = header, n.features = n.features, n.data = n.data, |
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285 i = i, ...), SDS = .readCtSDS(readfile = readfile, |
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286 n.data = n.data, i = i, nspots = nspots, ...), LightCycler = .readCtLightCycler(readfile = readfile, |
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287 n.data = n.data, i = i, nspots = nspots, ...), CFX = .readCtCFX(readfile = readfile, |
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288 n.data = n.data, i = i, nspots = nspots, ...), OpenArray = .readCtOpenArray(readfile = readfile, |
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289 n.data = n.data, i = i, nspots = nspots, ...), BioMark = .readCtBioMark(readfile = readfile, |
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290 n.data = n.data, i = i, nspots = nspots, ...)) |
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291 |
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292 data <- matrix(sample[, column.info[["Ct"]]], ncol = n.data[i]) |
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293 undeter <- apply(data, 2, function(x) x %in% c("Undetermined", |
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294 "No Ct")) |
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295 X.cat[, cols][undeter] <- "Undetermined" |
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296 nas <- c("Undetermined", "No Ct", "999", "N/A") |
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297 if (is.null(na.value)) { |
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298 data[data %in% nas | data == 0] <- NA |
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299 } |
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300 else { |
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301 data[data %in% nas | is.na(data) | data == 0] <- na.value |
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302 } |
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303 X[, cols] <- apply(data, 2, function(x) as.numeric(as.character(x))) |
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304 if ("flag" %in% names(column.info)) { |
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305 flags <- matrix(sample[, column.info[["flag"]]], |
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306 ncol = n.data[i]) |
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307 flags[flags == "-"] <- "Failed" |
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308 flags[flags == "+"] <- "Passed" |
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309 X.flags[, cols] <- flags |
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310 } |
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311 else { |
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312 X.flags[, cols] <- "Passed" |
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313 } |
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314 if (format == "OpenArray") { |
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315 s.names <- c(s.names, unique(sample$SampleInfo.SampleID)) |
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316 } |
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317 else if (format %in% c("EDS","plain", "SDS")) { |
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318 s.names <- c(s.names, unique(sample[, 2])) |
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319 } |
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320 else { |
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321 s.names <- s.names |
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322 } |
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323 if (i == 1) { |
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324 featPos <- paste("feature", 1:nspots, sep = "") |
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325 if ("position" %in% names(column.info)) |
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326 featPos <- as.character(sample[1:nspots, column.info[["position"]]]) |
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327 featType <- factor(rep("Target", nspots)) |
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328 if ("type" %in% names(column.info)) |
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329 featType <- sample[1:nspots, column.info[["type"]]] |
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330 featName <- paste("feature", 1:nspots, sep = "") |
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331 if ("feature" %in% names(column.info)) |
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332 featName <- as.character(sample[1:nspots, column.info[["feature"]]]) |
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333 df <- data.frame(featureNames = featName, featureType = as.factor(featType), |
185ba61836ab
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334 featurePos = featPos) |
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335 metaData <- data.frame(labelDescription = c("Name of the qPCR feature (gene)", |
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336 "Type pf feature", "Position on assay")) |
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337 featData <- AnnotatedDataFrame(data = df, varMetadata = metaData) |
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338 } |
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339 } |
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340 if (!missing(samples)) { |
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341 if (length(samples) < nsamples) { |
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342 warning("Not enough sample names provided; using Sample1, Sample2, ... instead\n") |
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343 samples <- paste("Sample", 1:nsamples, sep = "") |
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344 } |
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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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345 else if (length(samples) == nsamples) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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346 samples <- samples |
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planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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parents:
diff
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347 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
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348 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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349 else if (missing(samples)) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
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350 if (length(files) == nsamples) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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351 samples <- gsub("(.+)\\..+", "\\1", files) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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352 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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353 else if (length(s.names) == nsamples) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
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354 samples <- s.names |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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355 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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parents:
diff
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356 else { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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357 samples <- paste("Sample", 1:nsamples, sep = "") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
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358 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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359 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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360 samples <- make.unique(samples) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
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361 if (any(is.na(X))) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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362 warning("One or more samples contain NAs. Consider replacing these with e.g. Ct=40 now.") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
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363 if (missing(sample.info)) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
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364 pdata <- data.frame(sample = 1:length(samples), row.names = samples) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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365 sample.info <- new("AnnotatedDataFrame", data = pdata, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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366 varMetadata = data.frame(labelDescription = "Sample numbering", |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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367 row.names = "Sample names")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
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368 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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369 X.hist <- data.frame(history = capture.output(match.call(readCtData)), |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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370 stringsAsFactors = FALSE) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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371 out <- new("qPCRset", exprs = X, phenoData = sample.info, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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372 featureData = featData, featureCategory = X.cat, flag = X.flags, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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373 CtHistory = X.hist) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
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374 out |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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parents:
diff
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375 } |
2
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
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0
diff
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376 |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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parents:
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377 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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378 head(read.delim(file.path(path000, dpfiles), sep="\t")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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379 files <- read.delim(file.path(path000, dpfiles), sep="\t") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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380 switch(format, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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parents:
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381 "EDS"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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382 columns<- list(flag="EXPFAIL", feature="Target.Name", position="Well.Position", Ct="CT") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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parents:
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383 metadata <- data.frame(labelDescription = c("sampleName", "Treatment"), row.names = c("sampleName", "Treatment")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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parents:
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384 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
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385 rownames(phenoData)=as.vector(files$sampleName) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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386 raw<- readCtDataDav(files = as.vector(files$sampleName), header=TRUE, format="EDS", column.info=columns, path = path,sample.info=phenoData,n.features = as.numeric(nfeatures)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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387 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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388 "plain"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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389 metadata <- data.frame(labelDescription = c("sampleName", "Treatment"), row.names = c("sampleName", "Treatment")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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390 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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391 rownames(phenoData)=as.vector(files$sampleName) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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392 raw<- readCtDataDav(files = as.vector(files$sampleName), header=FALSE, format="plain", path = path, sample.info=phenoData,n.features = as.numeric(nfeatures)) |
185ba61836ab
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parents:
diff
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393 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
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diff
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394 "SDS"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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395 columns<- list(feature=3, Ct=6, flag=11) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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parents:
diff
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396 metadata <- data.frame(labelDescription = c("sampleName", "Treatment"), row.names = c("sampleName", "Treatment")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
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397 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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398 rownames(phenoData)=as.vector(files$sampleName) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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399 raw<- readCtDataDav(files = files$sampleName, format="SDS",column.info=columns, path = path, sample.info=phenoData, n.features=as.numeric(nfeatures)) |
185ba61836ab
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diff
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400 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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diff
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|
401 "LightCycler"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
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402 metadata <- data.frame(labelDescription = c("sampleName", "Treatment"), row.names = c("sampleName", "Treatment")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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403 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
404 rownames(phenoData)=as.vector(files$sampleName) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
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diff
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405 raw <- readCtDataDav(files = files$sampleName, path = path, format = "LightCycler", sample.info=phenoData,n.features = as.numeric(nfeatures)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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406 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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|
407 "CFX"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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408 metadata <- data.frame(labelDescription = c("sampleName", "Treatment"), row.names = c("sampleName", "Treatment")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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|
409 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
410 rownames(phenoData)=as.vector(files$sampleName) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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|
411 raw <- readCtDataDav(files = files$sampleName, path = path, format = "CFX", sample.info=phenoData,n.features = as.numeric(nfeatures)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
412 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
413 "OpenArray"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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414 metadata <- data.frame(labelDescription = c("sampleName", "Treatment"), row.names = c("sampleName", "Treatment")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
415 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
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416 rownames(phenoData)=as.vector(files$sampleName) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
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417 raw <- readCtDataDav(files = files$sampleName, path = path, format = "OpenArray", sample.info=phenoData,n.features = as.numeric(nfeatures)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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|
418 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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|
419 "BioMark"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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420 metadata <- data.frame(labelDescription = c("sampleName", "Treatment"), row.names = c("sampleName", "Treatment")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
421 phenoData <- new("AnnotatedDataFrame", data = files, varMetadata = metadata) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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422 rownames(phenoData)=as.vector(files$sampleName) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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423 raw <- readCtDataDav(files = files$sampleName, path = path, format = "BioMark", sample.info=phenoData, n.features = as.numeric(nfeatures)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
424 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
425 stop("Enter something that switches me!") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
426 ) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
427 cat("\n Files read correctly! ") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
428 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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429 write.table(exprs(raw), file=rawout, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
430 #################################################################################################################### |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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431 #Set a new categories for the values meeting two criterions |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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432 switch(format, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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433 "EDS"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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434 unreliable<-setCategory(raw, Ct.max=dcCtmax, Ct.min=dcCtmin,replicates=FALSE, flag=dcflag, flag.out="Y", quantile=NULL) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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435 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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436 "plain"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
437 unreliable<-setCategory(raw, Ct.max=dcCtmax, Ct.min=dcCtmin,replicates=FALSE, flag=dcflag, flag.out="Flagged", quantile=NULL) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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438 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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439 "SDS"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
440 unreliable<-setCategory(raw, Ct.max=dcCtmax, Ct.min=dcCtmin,replicates=FALSE, flag=dcflag, flag.out="TRUE", quantile=NULL) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
441 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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442 "LightCycler"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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443 unreliable<-setCategory(raw, Ct.max=dcCtmax, Ct.min=dcCtmin,replicates=FALSE, flag=dcflag, flag.out="Y", quantile=NULL) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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444 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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445 "CFX"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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446 unreliable<-setCategory(raw, Ct.max=dcCtmax, Ct.min=dcCtmin,replicates=FALSE, flag=dcflag, flag.out="Y", quantile=NULL) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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447 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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448 "OpenArray"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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449 unreliable<-setCategory(raw, Ct.max=dcCtmax, Ct.min=dcCtmin,replicates=FALSE, flag=dcflag, flag.out="TRUE ", quantile=NULL) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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450 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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451 "BioMark"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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452 unreliable<-setCategory(raw, Ct.max=dcCtmax, Ct.min=dcCtmin,replicates=FALSE, flag=dcflag, flag.out="Fail", quantile=NULL) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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453 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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454 stop("Enter something that switches me!") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
455 ) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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456 #unreliable<-setCategory(raw, Ct.max=dcCtmax, Ct.min=dcCtmin,replicates=FALSE, flag=dcflag, flag.out="Y", quantile=NULL) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
457 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
458 #################################################################################################################### |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
459 #Filter out the values of the new category |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
460 xFilter <- filterCategory(unreliable) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
461 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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462 cat("\n Categorization completed! ") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
463 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
464 png(x, # create PNG for the heat map |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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465 width = 10*300, # 5 x 300 pixels |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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466 height = 10*300, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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467 res = 300, # 300 pixels per inch |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
468 pointsize = 8) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
469 plotCtBoxes(xFilter, stratify=NULL, xlab = "Samples", ylab="Ct", names=as.character(seq(1, ncol(xFilter), 1))) # smaller font size |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
470 dev.off() |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
471 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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472 #write.table(exprs(xFilter), file=x, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
473 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
474 #################################################################################################################### |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
475 #NORMALIZATION |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
476 #method version 3.5.1 + Global mean |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
477 normalizeCtDataDav <- |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
478 function(q, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
479 norm = "deltaCt", |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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480 deltaCt.genes = NULL, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
481 scale.rank.samples, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
482 rank.type = "pseudo.median", |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
483 Ct.max = dcCtmax, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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484 geo.mean.ref, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
485 verbose = TRUE) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
486 { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
487 # Extract the data |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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488 data <- exprs(q) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
489 data.norm <- data |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
490 # Get the normalisation method |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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491 method <- match.arg(norm, c("quantile", "scale.rankinvariant", "norm.rankinvariant", "deltaCt", "geometric.mean", "globalmean")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
492 # Some general stuff that will be used by both rank.invariant methods |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
493 if (method %in% c("scale.rankinvariant", "norm.rankinvariant")) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
494 # Index to use for too high Ct values |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
495 #Ct.index <- data>Ct.max |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
496 data.Ctmax <- data |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
497 Ct.index <- is.na(data) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
498 #data.Ctmax[Ct.index] <- NA |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
499 data<-na.spline(data) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
500 # Define what to rank against |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
501 if (rank.type=="pseudo.median") { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
502 ref.data <- apply(data.Ctmax, 1, median, na.rm=TRUE) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
503 } else if (rank.type=="pseudo.mean") { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
504 ref.data <- apply(data.Ctmax, 1, mean, na.rm=TRUE) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
505 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
506 # Mark + replace NA values with something temporary |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
507 na.index <- is.na(ref.data) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
508 ref.data[na.index] <- 30 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
509 # Run the rank.invariant function |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
510 data.rankinvar <- apply(data, 2, normalize.invariantset, ref=ref.data) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
511 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
512 # The actual normalisation |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
513 switch(method, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
514 quantile = { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
515 # Use an internal limma function |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
516 data.norm <- normalizeQuantiles(data) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
517 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
518 scale.rankinvariant = { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
519 # Get all the rank invariant genes |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
520 ri.genes <- sapply(data.rankinvar, "[[", "i.set") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
521 # Remove those with too high Ct values |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
522 ri.genes[Ct.index] <- FALSE |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
523 # Remove those that were all NA for potentially other reasons |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
524 ri.genes[na.index,] <- FALSE |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
525 # Select those to use here |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
526 ri.count <- rowSums(ri.genes) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
527 if (missing(scale.rank.samples)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
528 scale.rank.samples <- ncol(data)-1 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
529 ri.index <- ri.count >= scale.rank.samples |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
530 if (sum(ri.index)==0) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
531 stop(paste("No rank invariant genes were found across", scale.rank.samples, "samples")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
532 # Extract the corresponding Ct values; average |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
533 ri.mean <- colMeans(data[ri.index,,drop=FALSE]) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
534 ri.scale <- ri.mean/ri.mean[1] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
535 # Correct the data |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
536 data.norm <- t(t(data)*ri.scale) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
537 # Print info |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
538 if (verbose) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
539 cat(c("Scaling Ct values\n\tUsing rank invariant genes:", paste(featureNames(q)[ri.index], collapse=" "), "\n")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
540 cat(c("\tScaling factors:", format(ri.scale, digits=3), "\n")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
541 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
542 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
543 norm.rankinvariant = { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
544 # Print info |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
545 if (verbose) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
546 cat("Normalizing Ct values\n\tUsing rank invariant genes:\n") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
547 # Correct the data based on the calculations above |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
548 for (i in 1:ncol(data)) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
549 # Check if there are any rank invariant genes |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
550 ri.sub <- data.rankinvar[[i]] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
551 ri.genes <- ri.sub[["i.set"]] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
552 # Remove those that don't pass the Ct.max criteria |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
553 ri.genes[Ct.index[,i]] <- FALSE |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
554 # Remove those that are NA for other reasons |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
555 ri.genes[na.index] <- FALSE |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
556 if (sum(ri.genes)==0) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
557 warning(paste("\tNo rank invariant genes were found for sample ", sampleNames(q)[i], "; sample not normalized\n", sep="")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
558 next |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
559 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
560 # If verbose, print some info |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
561 if (verbose) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
562 cat(paste("\t", sampleNames(q)[i], ": ", sum(ri.genes), " rank invariant genes\n", sep="")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
563 # The actual correction |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
564 data.norm[,i] <- as.numeric(approx(ri.sub$n.curve$y, ri.sub$n.curve$x, xout=data[,i], rule=2)$y) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
565 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
566 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
567 deltaCt = { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
568 # Which are the reference genes (endogenous controls) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
569 if (is.null(deltaCt.genes)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
570 deltaCt.genes <- unique(featureNames(q)[featureType(q)=="Endogenous Control"]) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
571 c.index <- featureNames(q) %in% deltaCt.genes |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
572 if (verbose) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
573 cat(c("Calculating deltaCt values\n\tUsing control gene(s):", paste(deltaCt.genes, collapse=" "), "\n")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
574 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
575 # Run though all cards; perform internal normalisation |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
576 for (c in 1:ncol(data)) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
577 # Calculate the control genes |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
578 refCt <- mean(data[c.index,c], na.rm=TRUE) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
579 refsd <- sd(data[c.index,c], na.rm=TRUE) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
580 # Difference for target and controls |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
581 data.norm[,c] <- data[,c]-refCt |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
582 # Print results |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
583 if (verbose) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
584 cat(paste("\tCard ", c, ":\tMean=", format(refCt, dig=4), "\tStdev=", format(refsd, dig=3), "\n", sep="")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
585 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
586 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
587 geometric.mean = { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
588 # For each column, calculate the geometric mean of Ct values<Ct.max |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
589 #geo.mean <- apply(data, 2, function(x) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
590 # xx <- log2(subset(x, x<Ct.max)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
591 # 2^mean(xx)}) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
592 geo.mean <- apply(data, 2, function(x) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
593 xx <- subset(x, x<=Ct.max) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
594 geometric.mean(xx)}) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
595 # Which sample to scale to |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
596 #if (missing(geo.mean.ref)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
597 # geo.mean.ref <- 1 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
598 # Calculate the scaling factor |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
599 #geo.scale <- geo.mean/geo.mean[geo.mean.ref] |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
600 # Adjust the data accordingly |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
601 data.norm <- t(t(data) - geo.mean) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
602 if (verbose) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
603 cat(c("Scaling Ct values\n\tUsing geometric mean within each sample\n")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
604 #cat(c("\tScaling factors:", format(geo.scale, digits=3), "\n")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
605 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
606 } # switch |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
607 ,globalmean = { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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608 glo <- apply(data, 2, function(x) { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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609 xx <- subset(x, x <= Ct.max) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
610 mean(xx) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
611 }) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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612 data.norm <- t(t(data) - glo) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
613 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
614 ) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
615 # Replace with the normalised Ct exprs |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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616 exprs(q) <- data.norm |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
617 # Add to the history of the object |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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618 if (nrow(getCtHistory(q))==0) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
619 setCtHistory(q) <- data.frame(history="Manually created qPCRset object.", stringsAsFactors=FALSE) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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620 setCtHistory(q) <- rbind(getCtHistory(q), capture.output(match.call(normalizeCtData))) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
621 # Return the normalised object |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
622 q |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
623 } |
2
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
parents:
0
diff
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624 #library(NormqPCR) |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
625 |
2
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
parents:
0
diff
changeset
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626 #delete.na <- function(DF, n=0) { |
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
parents:
0
diff
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627 # DF[rowSums(is.na(DF)) <= n,] |
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
parents:
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diff
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628 #} |
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
parents:
0
diff
changeset
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629 |
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
parents:
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diff
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630 #user_number=5 |
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
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diff
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631 #genorm <- selectHKs(t(delete.na(as.matrix(exprs(xGlico)),0)), method = "geNorm", Symbols = rownames(as.matrix(delete.na(exprs(xGlico),0))), minNrHK = as.numeric(user_number), log = TRUE) |
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
parents:
0
diff
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632 #normfinder <- selectHKs(as.matrix(t(delete.na(exprs(xGlico),0))), group= files$Treatment , method = "NormFinder", Symbols =rownames(as.matrix(delete.na(exprs(xGlico),0))), minNrHK = as.numeric(user_number), log = TRUE) |
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
parents:
0
diff
changeset
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633 #intersection= intersect(normfinder$ranking, genorm$ranking[1:as.numeric(user_number)]) |
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
parents:
0
diff
changeset
|
634 |
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
parents:
0
diff
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635 #cat("\n GeNorm and NormFinder transcripts selected as housekeeping for normalization! \n") |
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
parents:
0
diff
changeset
|
636 #intersection |
6cd22b1fbf6d
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 18d030f0c2e423a04617a3827ba5a652c8d7867a
davidecangelosi
parents:
0
diff
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637 #dnorm <- normalizeCtData(xGlico , norm="deltaCt", deltaCt.genes=as.vector(intersection)) |
0
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
638 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
639 switch(normalizationMethod, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
640 "deltaCt"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
641 normalizedDataset <- normalizeCtDataDav(xFilter, norm="deltaCt", deltaCt.genes =explode(normalizers, sep = ",")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
642 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
643 "quantile"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
644 normalizedDataset <- normalizeCtDataDav(xFilter, norm=normalizationMethod) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
645 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
646 "scale.rankinvariant"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
647 normalizedDataset <- normalizeCtDataDav(xFilter, norm=normalizationMethod) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
648 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
649 "norm.rankinvariant"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
650 normalizedDataset <- normalizeCtDataDav(xFilter, norm=normalizationMethod) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
651 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
652 "geometric.mean"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
653 normalizedDataset <- normalizeCtDataDav(xFilter, norm=normalizationMethod) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
654 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
655 "globalmean"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
656 normalizedDataset <- normalizeCtDataDav(xFilter, norm=normalizationMethod) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
657 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
658 stop("Enter something that switches me!") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
659 ) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
660 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
661 #if (normalizationMethod=="deltaCt") { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
662 #normalize CT data |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
663 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
664 #normalizedDataset <- normalizeCtDataDav(xFilter, norm="deltaCt", deltaCt.genes =explode(normalizers, sep = ",")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
665 #} else { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
666 #normalizedDataset <- normalizeCtDataDav(xFilter, norm=normalizationMethod) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
667 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
668 #} |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
669 cat("\n Data normalized correctly! \n") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
670 write.table(exprs(normalizedDataset), file=outputNorm, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
671 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
672 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
673 #normalizedDataset |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
674 #################################################################################################################### |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
675 #Check noise reduction by empirical cumulative distribution |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
676 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
677 #X = rnorm(100) # X is a sample of 100 normally distributed random variables |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
678 # P = ecdf(X) # P is a function giving the empirical CDF of X |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
679 #Y = rnorm(1000) # X is a sample of 100 normally distributed random variables |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
680 # PY = ecdf(Y) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
681 #plotâ„— |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
682 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
683 #lines(PY) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
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|
684 png(outputECDF, # create PNG for the heat map |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
685 width = 10*300, # 5 x 300 pixels |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
686 height = 10*300, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
687 res = 300, # 300 pixels per inch |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
688 pointsize = 8) # smaller font size |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
689 vec=c() |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
690 for (i in 1:nrow(exprs(xFilter))){ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
691 CVX<-(sd(2^-exprs(xFilter)[i,], na.rm = TRUE)/mean(2^-exprs(xFilter)[i,], na.rm = TRUE))*100 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
692 vec=c(vec, c(CVX)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
693 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
694 vec<-na.omit(vec) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
695 P = ecdf(vec) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
696 gm=c() |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
697 for (i in 1:nrow(exprs(normalizedDataset))){ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
698 CVGM<-(sd(2^-exprs(normalizedDataset)[i,], na.rm = TRUE)/mean(2^-exprs(normalizedDataset)[i,], na.rm = TRUE))*100 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
699 gm=c(gm, c(CVGM)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
700 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
701 gm<-na.omit(gm) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
702 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
703 PY = ecdf(gm) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
704 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
705 plot_colors <- c(rgb(r=0.0,g=0.0,b=0.9), "red", "forestgreen",rgb(r=0.0,g=0.0,b=0.0),rgb(r=0.5,g=0.0,b=0.3),rgb(r=0.0,g=0.4,b=0.4)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
706 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
707 plot(P,col=plot_colors[1],xlim=c(0.0,600), ylim=c(0.0,1),xaxp = c(0.0, 600, 6),yaxp = c(0.0, 1, 10), cex=1.3, lwd=5, main=NULL,xlab="CV(%)",ylab="Empirical Cumulative Distribution") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
708 lines(PY, lwd=5, col=plot_colors[6],cex=1.3) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
709 legend("bottomright", c("not normalized", "normalized"), cex=1.3, col=c(plot_colors[1],plot_colors[6]), lwd=c(5,5)); |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
710 dev.off() |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
711 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
712 #Two-sample Kolmogorov-Smirnov |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
713 ks.test(vec,gm) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
714 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
715 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
716 #write.table(exprs(qFiltNAs), file=outputIMP, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
717 png(outputIMP, # create PNG for the heat map |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
718 width = 10*300, # 5 x 300 pixels |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
719 height = 10*300, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
720 res = 300, # 300 pixels per inch |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
721 pointsize = 8) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
722 plotCtBoxes(normalizedDataset, stratify=NULL, xlab = "Samples", ylab="DeltaCt", names=as.character(seq(1, ncol(normalizedDataset), 1))) # smaller font size |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
723 dev.off() |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
724 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
725 ################################################## Filtering based on number of NAs################################################## |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
726 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
727 #FILTERING on the basis of NAs |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
728 #qPCRset.R |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
729 setMethod("exprs", signature(object="qPCRset"), definition = |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
730 function (object) {x <- assayDataElement(object, "exprs"); rownames(x) <- featureNames(object); colnames(x) <- sampleNames(phenoData(object));x} |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
731 ) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
732 ncatn <- as.integer(n.samples(normalizedDataset))*as.integer(percentofnastoremove)/100 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
733 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
734 qFiltNAs <- filterCtData(normalizedDataset, remove.category=c("Undetermined","Unreliable"), n.category=as.integer(ncatn),remove.name=explode(filtnames, sep = ",")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
735 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
736 cat("\n Data filtered correctly! \n") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
737 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
738 if (is.na(exprs(qFiltNAs))){ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
739 switch(imputeMethod, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
740 "knn"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
741 imp<-impute.knn(exprs(qFiltNAs) ,k = as.integer(kappa), maxp = as.integer(macsp), rng.seed=362436069) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
742 exprs(qFiltNAs)=imp$data |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
743 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
744 "mestdagh"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
745 #Mesdagh |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
746 #sostituisce a NA -1000 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
747 for (i in 1:nrow(exprs(qFiltNAs))){ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
748 for(j in 1:ncol(exprs(qFiltNAs))){ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
749 if(is.na(exprs(qFiltNAs)[i,j])>0)exprs(qFiltNAs)[i,j]<- -1000 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
750 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
751 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
752 temp<-exprs(qFiltNAs) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
753 for (i in 1:nrow(exprs(qFiltNAs))){ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
754 for(j in 1:ncol(exprs(qFiltNAs))){ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
755 if(exprs(qFiltNAs)[i,j]<(-100))exprs(qFiltNAs)[i,j]<- max(temp[i,])+1 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
756 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
757 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
758 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
759 "cubic"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
760 exprs(qFiltNAs) <- na.spline(exprs(qFiltNAs)) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
761 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
762 "mean"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
763 exprs(qFiltNAs)<-impute(exprs(qFiltNAs),mean) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
764 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
765 "median"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
766 exprs(qFiltNAs)<-impute(exprs(qFiltNAs),median) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
767 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
768 "nondetects"={ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
769 qFiltNAs <- qpcrImpute(qFiltNAs, outform=c("Single"),linkglm = c("logit")) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
770 }, |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
771 stop("Enter something that switches me!") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
772 ) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
773 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
774 cat("\n Imputation completed! \n") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
775 }else{ |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
776 cat("\n Nothing to impute! \n") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
777 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
778 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
779 write.table(exprs(qFiltNAs), file=outputRemaining, quote=FALSE, row.names=TRUE, col.names=TRUE, sep = "\t") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
780 |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
781 if (DEAMethod=="ttest") { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
782 #Differential expression analysis (paired t test+BH). Returns Fold change in linear scale. |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
783 DEG<-ttestCtData(qFiltNAs, groups = files$Treatment, alternative = alternative, paired = ifelse(paired=="TRUE", TRUE, FALSE), replicates =ifelse(replicates=="TRUE", TRUE, FALSE), sort=ifelse(sort=="TRUE", TRUE, FALSE), stringent=ifelse(stringent=="TRUE", TRUE, FALSE), p.adjust=padjust) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
784 write.table(DEG, file=outputDEA, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
785 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
786 if (DEAMethod=="rp") { |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
787 DEG<-RP(exprs(qFiltNAs), as.numeric(pData(qFiltNAs)$Treatment)-1, num.perm = 1000,logged = TRUE, gene.names = featureNames(qFiltNAs), huge=TRUE, plot = FALSE, rand = 123) |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
788 write.table(DEG[1:5], file=outputDEA, quote=FALSE, row.names=TRUE, col.names=TRUE,sep = "\t") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
789 } |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
|
790 cat("\n Differential expression analysis completed correctly! \n") |
185ba61836ab
planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit 04049039da97e1c9a8048e732afca48f2741cadf
davidecangelosi
parents:
diff
changeset
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791 cat("\n Workflow ended correctly! \n") |