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comparison SMART/DiffExpAnal/DESeqTools/exportDiff.R @ 18:94ab73e8a190

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author m-zytnicki
date Mon, 29 Apr 2013 03:20:15 -0400
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17:b0e8584489e6 18:94ab73e8a190
1 # exportDiff
2 # export differentially expressed genes
3
4 # input : complete, alpha, adjMethod, projectName
5 # output : diff genes, up and down in xls files
6
7 # created Feb 14th, 2012
8
9
10 exportDiff <- function( complete, alpha, adjMethod, OUT_upName, OUT_downName, out = T ){
11
12 diff <- complete[which(complete[,grep("adjp",colnames(complete))] < alpha),]
13
14 gup <- up( diff )
15 gdown <- down( diff )
16
17 if (out){
18 gup[,(ncol(gup)-4):ncol(gup)] <- format( gup[,(ncol(gup)-4):ncol(gup)], digits=3, dec=",")
19 gdown[,(ncol(gdown)-4):ncol(gdown)] <- format( gdown[,(ncol(gdown)-4):ncol(gdown)], digits=3, dec=",")
20 write.table(gup, file=OUT_upName, row.names=F, sep="\t")
21 write.table(gdown, file=OUT_downName, row.names=F, sep="\t")
22 }
23 return( diff )
24 }
25
26
27 up <- function( diff ){
28
29 up <- diff[diff$log2FC > 0,]
30 up <- up[order(up[,grep("adjp",colnames(up))]),]
31
32 return( up )
33 }
34
35
36 down <- function( diff ){
37
38 down <- diff[diff$log2FC < 0,]
39 down <- down[order(down[,grep("adjp",colnames(down))]),]
40
41 return( down )
42 }