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