Mercurial > repos > vmarcon > normalization

annotate normalization.R @ 0:79f00bc83ecc draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
author vmarcon
date Thu, 18 Jan 2018 06:20:30 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
1 # R Script implementing different kind of normalisation
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
2 # Input : a file containing a table with numeric values
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
3 # except for the first column containing sample names
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
4 # and the first line containing variable names
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
5 # separator expected is <TAB>
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
6 #
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
7 # Normalization method :
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
8 # log, DESeq2, Rlog, Standard_score, Pareto, TSS, TSS+CLR, Pareto
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
9 #
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
10 # Ouptut : input table with values normalized according
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
11 # to the normalization procedure chosen
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
12 #-----------------------------------------------------------------
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
13 # Authors : luc.jouneau(at)inra.fr
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
14 # valentin.marcon(at)inra.fr
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
15 # Version : 0.9
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
16 # Date : 30/08/2017
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
17 #-----------------------------------------------------------------
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
18
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
19 normalization=function(
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
20 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
21 # Function input
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
22 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
23 #Possible values : "log", "DESeq2", "Rlog", "Standard_score", "Pareto", "TSS", "TSS_CLR"
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
24 transformation_method="Standard_score",
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
25 na_encoding="NA",
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
26 #Path to file containg table of values (separator="tab")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
27 input_file="",
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
28 #Path to file produced after transformation
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
29 output_file="out/table_out.txt",
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
30 #Path to file containing messages for user if something bad happens
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
31 log_file="log/normalization_report.html",
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
32 #Boolean flag (0/1) indicating if variables are in line or in columns
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
33 variable_in_line="1") {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
34
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
35 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
36 # Read and verify data
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
37 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
38 #1°) Checks valids for all modules
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
39 if (variable_in_line=="1") {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
40 column_use="individual"
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
41 line_use="variable"
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
42 } else {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
43 line_use="individual"
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
44 column_use="variable"
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
45 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
46 log_error=function(message="") {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
47 cat("<HTML><HEAD><TITLE>Normalization report</TITLE></HEAD><BODY>\n",file=log_file,append=F,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
48 cat("&#9888 An error occurred while trying to read your table.\n<BR>",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
49 cat("Please check that:\n<BR>",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
50 cat("<UL>\n",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
51 cat(" <LI> the table you want to process contains the same number of columns for each line</LI>\n",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
52 cat(" <LI> the first line of your table is a header line (specifying the name of each ",column_use,")</LI>\n",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
53 cat(" <LI> the first column of your table specifies the name of each ",line_use,"</LI>\n",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
54 cat(" <LI> both individual and variable names should be unique</LI>\n",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
55 cat(" <LI> each value is separated from the other by a <B>TAB</B> character</LI>\n",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
56 cat(" <LI> except for first line and first column, table should contain a numeric value</LI>\n",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
57 cat(" <LI> this value may contain character '.' as decimal separator or '",na_encoding,"' for missing values</LI>\n",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
58 cat("</UL>\n",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
59 cat("-------<BR>\nError messages recieved :<BR><FONT color=red>\n",conditionMessage(message),"</FONT>\n",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
60 cat("</BODY></HTML>\n",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
61 q(save="no",status=1)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
62 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
63
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
64 tab_in=tryCatch(
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
65 {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
66 tab_in=read.table(file=input_file,sep="\t",header=T,quote="\"",na.strings=na_encoding,check.names=FALSE)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
67 },
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
68 error=function(cond) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
69 log_error(message=cond)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
70 return(NA)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
71 },
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
72 warning=function(cond) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
73 log_error(message=cond)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
74 return(NA)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
75 },
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
76 finally={
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
77 #Do nothing special
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
78 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
79 )
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
80
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
81 if (ncol(tab_in)<2) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
82 log_error(simpleCondition("The table you want to normalize contains less than two columns."))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
83 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
84
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
85 rn=as.character(tab_in[,1])
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
86 if (length(rn)!=length(unique(rn))) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
87 duplicated_rownames=table(rn)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
88 duplicated_rownames=duplicated_rownames[duplicated_rownames>1]
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
89 duplicated_rownames=names(duplicated_rownames)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
90 if (length(duplicated_rownames)>3) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
91 duplicated_rownames=c(duplicated_rownames[1:3],"...")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
92 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
93 duplicated_rownames=paste(duplicated_rownames,collapse=", ")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
94 log_error(simpleCondition(
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
95 paste("The table you want to normalize have duplicated values in the first column (",
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
96 line_use," names) - duplicated ",line_use," names : ",duplicated_rownames,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
97 ))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
98 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
99 tab=tab_in[,-1]
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
100 rownames(tab)=rn
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
101
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
102 #Check all columns are numeric
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
103 tab=as.matrix(tab)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
104 cell.with.na=c()
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
105 for (i in 1:ncol(tab)) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
106 na.v1=is.na(tab[,i])
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
107 na.v2=is.na(as.numeric(tab[,i]))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
108 if (sum(na.v1)!=sum(na.v2)) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
109 sel=which(na.v1!=na.v2)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
110 sel=sel[1]
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
111 value=tab[sel,i]
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
112 log_error(simpleCondition(
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
113 paste("Column '",colnames(tab)[i],"' of your table contains non numeric values. Please check its content (on line #",sel," : value='",value,"').",sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
114 ))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
115 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
116 if (length(cell.with.na)==0 & sum(na.v1)!=0) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
117 cell.with.na=c(i,which(na.v1)[1])
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
118 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
119 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
120
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
121 #2°) Checks only valid for normalization module
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
122 if (transformation_method %in% c("DESeq2","Rlog")) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
123 #Check there is no missing values
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
124 if (length(cell.with.na)!=0) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
125 log_error(simpleCondition(
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
126 paste("Column '",colnames(tab)[cell.with.na[1]],"' of your table contains missing values (see line #",cell.with.na[2],").\n",
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
127 transformation_method," normalization does not accept missing values. ",sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
128 ))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
129 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
130 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
131 if (transformation_method %in% c("DESeq2","Rlog","TSS","TSS_CLR")) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
132 #Check values are integer
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
133 for (i in 1:ncol(tab)) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
134 if (!is.integer(tab[,i])) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
135 sel=which(!is.integer(tab[,i]))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
136 sel=sel[1]
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
137 value=tab[sel,i]
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
138 log_error(simpleCondition(
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
139 paste("Column '",colnames(tab)[i],"' of your table contains non integer values.\n",
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
140 transformation_method," normalization only accepts integer values. ",
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
141 "Please check its content (on line #",sel," : value=",value,").",sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
142 ))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
143 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
144 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
145 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
146
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
147 if (transformation_method %in% c("log","TSS","TSS_CLR","DESeq2","Rlog")) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
148 #Check values are positive
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
149 for (i in 1:ncol(tab)) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
150 if (sum(tab[,i]>=0 | is.na(tab[,i]))!=nrow(tab)) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
151 sel=which(tab[,i]<0)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
152 sel=sel[1]
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
153 value=tab[sel,i]
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
154 log_error(simpleCondition(
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
155 paste("Column '",colnames(tab)[i],"' of your table contains negative values.\n",
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
156 transformation_method," normalization only accepts positive or null values. ",
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
157 "Please check its content (on line #",sel," : value=",value,").",sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
158 ))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
159 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
160 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
161 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
162
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
163 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
164 # End of data checks
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
165 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
166
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
167 ### Transpose if variable are in line ###
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
168 if (variable_in_line=="1") {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
169 #Transpose matrix
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
170 tab=t(tab)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
171 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
172
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
173 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
174 ### Value transformation
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
175 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
176
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
177 #Avoid null values when there is a log transformation
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
178 na.replaced=c()
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
179 log.transformed=FALSE
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
180 if (transformation_method %in% c("log","TSS_CLR")) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
181 log.transformed=TRUE
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
182 for (idx_col in 1:ncol(tab)) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
183 sel=tab[,idx_col]==0
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
184 na.replaced=cbind(na.replaced,sel)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
185 tab[sel,idx_col]=1e-2
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
186 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
187 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
188
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
189 ### log ###
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
190 if (transformation_method=="log") {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
191 tab=log2(tab)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
192 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
193
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
194 ### DESeq2 or Rlog ###
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
195 if (transformation_method %in% c("DESeq2","Rlog")) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
196 library(DESeq2)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
197 n <- ncol(tab)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
198 dds <- DESeqDataSetFromMatrix(tab,
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
199 colData = data.frame(condition = c("a", rep("b", n - 1))),
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
200 design = formula(~ condition))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
201 colnames(dds) <- colnames(tab)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
202 dds <- estimateSizeFactors(dds)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
203 tab <- switch(transformation_method,
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
204 DESeq2 = counts(dds, normalized = TRUE),
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
205 Rlog = assay(rlogTransformation(dds))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
206 )
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
207 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
208
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
209 ### Standard_score ###
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
210 if (transformation_method=="Standard_score") {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
211 tab=scale(tab)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
212 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
213
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
214 ### Pareto ###
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
215 if (transformation_method=="Pareto") {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
216 tab.centered <- apply(tab, 2, function(x) x - mean(x,na.rm=TRUE))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
217 tab.sc <- apply(tab.centered, 2, function(x) x/sqrt(sd(x,na.rm=TRUE)))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
218 tab=tab.sc
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
219 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
220
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
221 ### TSS ###
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
222 if (transformation_method=="TSS") {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
223 tab= t(apply(tab, 1, function(x) x/sum(x,na.rm=TRUE)))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
224 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
225
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
226 ### TSS + CLR avec function de mixOmics ###
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
227 if (transformation_method=="TSS_CLR") {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
228 #From http://stackoverflow.com/questions/2602583/geometric-mean-is-there-a-built-in
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
229 geometric.mean = function(x, na.rm=TRUE){
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
230 exp(sum(log(x[x > 0]), na.rm=na.rm) / length(x))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
231 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
232 tab = t(apply(tab+1e-2,1,function(x) log(x/geometric.mean(x,na.rm=TRUE))))
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
233 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
234
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
235
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
236 #If there is a log transformation put 0 where there was NA
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
237 if (log.transformed) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
238 for (idx_col in 1:ncol(tab)) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
239 tab[na.replaced[,idx_col],idx_col]=0
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
240 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
241 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
242
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
243 #If there are missing values, replace it with NA_enconding
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
244 for (idx_col in 1:ncol(tab)) {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
245 sel=is.na(tab[,idx_col])
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
246 tab[sel,idx_col]=na_encoding
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
247 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
248
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
249 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
250 # Prepare and write output table
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
251 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
252 if (variable_in_line=="1") {
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
253 #Transpose matrix again
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
254 tab=t(tab)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
255 }
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
256
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
257 tab_out=cbind(rownames(tab),tab)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
258 colnames(tab_out)[1]=colnames(tab_in)[1]
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
259
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
260 write.table(file=output_file,tab_out,sep="\t",row.names=F,quote=F)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
261
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
262 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
263 # Treatment successfull
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
264 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
265 cat("<HTML><HEAD><TITLE>Normalization report</TITLE></HEAD><BODY>\n",file=log_file,append=F,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
266 cat(paste("&#10132; You choose to apply the transformation method :",transformation_method,"<BR>"),file=log_file,append=F,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
267 cat("&#10003; Your normalization process is successfull !<BR>",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
268 cat("</BODY></HTML>\n",file=log_file,append=T,sep="")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
269
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
270 q(save="no",status=0)
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
271
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
272 } # end of function
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
273
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
274 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
275 # Test
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
276 ##########################################################
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
277 #Used for debug : LJO 6/3/2017
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
278 #normalization()
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
279 #setwd("H:/INRA/cati/groupe stats/Galaxy/normalisation")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
280 #normalization(transformation_method="Standard_score",na_encoding="NA",input_file="datasets/valid - decathlon.txt",output_file="out/table_out.txt",log_file="log/normalization.html",variable_in_line="0")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
281 #normalization(transformation_method="Pareto",na_encoding="NA",input_file="datasets/valid - decathlon.txt",output_file="out/table_out.txt",log_file="log/normalization.html",variable_in_line="1")
79f00bc83ecc planemo upload commit a2411926bebc2ca3bb31215899a9f18a67e59556
vmarcon
parents:
diff changeset
282