Mercurial > repos > laurenmarazzi > netisce_test
comparison tools/myTools/bin/crit2.R @ 1:7e5c71b2e71f draft default tip
Uploaded
author | laurenmarazzi |
---|---|
date | Wed, 22 Dec 2021 16:00:34 +0000 |
parents | |
children |
comparison
equal
deleted
inserted
replaced
0:f24d4892aaed | 1:7e5c71b2e71f |
---|---|
1 #!/usr/bin/env Rscript | |
2 .libPaths('~/R_libs_36') | |
3 args = commandArgs(trailingOnly=TRUE) | |
4 | |
5 library(plyr) | |
6 library("dplyr", warn.conflicts = FALSE) | |
7 library(reshape2) | |
8 library(readr) | |
9 getwd() | |
10 | |
11 exp<-read.delim(args[1],sep=" ",row.names = 1) | |
12 samples<-read.delim(args[2],sep="\t",row.names = 1) | |
13 exp<-exp %>% dplyr::filter(row.names(exp) %in% row.names(samples)) | |
14 desired<-args[3] | |
15 undesired<-args[4] | |
16 filter<-args[5] | |
17 | |
18 | |
19 dfdes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% desired,,drop=FALSE])) | |
20 meandes<- apply(dfdes,2,mean) | |
21 dfundes<- exp %>% filter(rownames(exp) %in% rownames(samples[samples$phenotype %in% undesired,,drop=FALSE])) | |
22 meandundes<-apply(dfundes,2,mean) | |
23 test<-meandes-meandundes | |
24 disc<-test | |
25 disc[disc<0]<-0 | |
26 disc[disc>0]<-1 | |
27 nodes<-colnames(dfdes) | |
28 | |
29 is<-read.delim(args[6],sep=" ") #internal_markers.txt | |
30 isdisc<-is | |
31 if (filter=="strict"){ | |
32 for (node in nodes){ | |
33 if (disc[node]==0){ | |
34 val=max(dfdes[,node]) | |
35 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0) | |
36 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1) | |
37 } | |
38 if (disc[node]==1){ | |
39 val=min(dfdes[,node]) | |
40 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1) | |
41 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0) | |
42 } | |
43 } | |
44 }else { #filter=="relaxed" | |
45 for (node in nodes){ | |
46 if (disc[node]==0){ | |
47 val=min(dfundes[,node]) | |
48 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0) | |
49 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1) | |
50 } | |
51 if (disc[node]==1){ | |
52 val=max(dfdes[,node]) | |
53 isdisc[,node]<-replace(isdisc[,node],is[,node]>val, 1) | |
54 isdisc[,node]<-replace(isdisc[,node],is[,node]<val, 0) | |
55 } | |
56 } | |
57 | |
58 } | |
59 | |
60 | |
61 | |
62 hammings<-data.frame(isdisc$replicate,isdisc$perturbation) | |
63 colnames(hammings)=c("replicate","perturbation") | |
64 hammings$hammingdist<-sapply(isdisc[,3],function(x) sum(disc != x)) | |
65 | |
66 if (length(nodes)<10){ | |
67 hams1_1<-hammings %>%filter(hammingdist<1) | |
68 }else{ | |
69 hams1_1<-hammings %>%filter(hammingdist<=length(nodes)-round(.9*length(nodes))) | |
70 } | |
71 | |
72 write.table(hams1_1[,c(1,2)],'crit2_perturbations.txt',quote=FALSE,row.names = FALSE,sep=" ") | |
73 | |
74 |