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author | yufei-luo |
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date | Mon, 13 May 2013 10:06:30 -0400 |
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# exportDiff # export differentially expressed genes # input : complete, alpha, adjMethod, projectName # output : diff genes, up and down in xls files # created Feb 14th, 2012 # Marie-Anges Dillies exportDiff <- function( complete, alpha, adjMethod, OUT_upName, OUT_downName, out = T ){ diff <- complete[which(complete[,grep("adjp",colnames(complete))] < alpha),] gup <- up( diff ) gdown <- down( diff ) if (out){ gup[,(ncol(gup)-4):ncol(gup)] <- format( gup[,(ncol(gup)-4):ncol(gup)], digits=3, dec=",") gdown[,(ncol(gdown)-4):ncol(gdown)] <- format( gdown[,(ncol(gdown)-4):ncol(gdown)], digits=3, dec=",") write.table(gup, file=OUT_upName, row.names=F, sep="\t") write.table(gdown, file=OUT_downName, row.names=F, sep="\t") } return( diff ) } up <- function( diff ){ up <- diff[diff$log2FC > 0,] up <- up[order(up[,grep("adjp",colnames(up))]),] return( up ) } down <- function( diff ){ down <- diff[diff$log2FC < 0,] down <- down[order(down[,grep("adjp",colnames(down))]),] return( down ) }