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remove projectID
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@kvaldez
kvaldez committed Aug 2, 2018
1 parent d95d648 commit 2fbfb1d
Showing 1 changed file with 15 additions and 15 deletions.
30 changes: 15 additions & 15 deletions MAAPster_functions.R
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
projectId = 'testing'
# projectId = 'testing'
#### 1) Process GEO files function takes gseid and returns ExpressionFeatureSet object ####
processGEOfiles <- function(id,listGroups){
library(GEOquery)
Expand Down Expand Up @@ -277,12 +277,12 @@ deg = function(norm, listContrasts) {
all$FC = ifelse(all$logFC<0, -1/(2^all$logFC), 2^all$logFC) #add fold change and rearrange columns
all = all[,c(9,12,2,5,6,3,8,10,11,1,4,7)]
# Write out to a file
write.table(all,file=paste(projectId,"_",cons[i],"_all_genes.txt",sep=""),sep="\t",row.names=F)
write.table(all,file=paste(cons[i],"_all_genes.txt",sep=""),sep="\t",row.names=F)
listDEGs[[i]]=all
}
names(listDEGs)=cons
norm_annotated <- merge(exprs(norm), Annot,by.x=0, by.y=0, all.x=T) #write out normalized annotated data
y<-paste("_",projectId, sep="")
y<-paste("_", sep="")
tNorm = tempfile(pattern = "normalized_data_", tmpdir = getwd(), fileext = paste0(y,'.txt'))
write.table(norm_annotated,file=tNorm,sep="\t",row.names=F)
for (i in 1:length(listDEGs)) { #Volcano plots
Expand Down Expand Up @@ -332,31 +332,31 @@ pathways = function(degs,species) {
fin.dw$SYMBOL = as.character(fin.dw$SYMBOL)
if (species=='human')
{
cat(fin.up$SYMBOL,file=(paste0(projectId,'_',names(degs$listDEGs[i]),'_Top500_Up.txt')), sep='\n')
cat(fin.dw$SYMBOL,file=(paste0(projectId,'_',names(degs$listDEGs[i]),'_Top500_Down.txt')),sep='\n')
cat(fin.up$SYMBOL,file=(paste0('_',names(degs$listDEGs[i]),'_Top500_Up.txt')), sep='\n')
cat(fin.dw$SYMBOL,file=(paste0('_',names(degs$listDEGs[i]),'_Top500_Down.txt')),sep='\n')
}
else
{
cat(fin.up$SYMBOL,file=paste0(names(degs$listDEGs[i]),"_Top500temp_Up.txt"),sep='\n')
cat(fin.dw$SYMBOL,file=paste0(names(degs$listDEGs[i]),"_Top500temp_Dw.txt"),sep='\n')

system(paste0("cat ",names(degs$listDEGs[i]),"_Top500temp_Up.txt | grep -v \"^NA\" | ./m2h | grep -v XXXX | cut -f2 -d\" \" >",projectId,'_',names(degs$listDEGs[i]),"_Top500_Up.txt"))
system(paste0("cat ",names(degs$listDEGs[i]),"_Top500temp_Dw.txt | grep -v \"^NA\" | ./m2h | grep -v XXXX | cut -f2 -d\" \" >",projectId,'_',names(degs$listDEGs[i]),"_Top500_Down.txt"))
system(paste0("cat ",names(degs$listDEGs[i]),"_Top500temp_Up.txt | grep -v \"^NA\" | ./m2h | grep -v XXXX | cut -f2 -d\" \" >",'_',names(degs$listDEGs[i]),"_Top500_Up.txt"))
system(paste0("cat ",names(degs$listDEGs[i]),"_Top500temp_Dw.txt | grep -v \"^NA\" | ./m2h | grep -v XXXX | cut -f2 -d\" \" >",'_',names(degs$listDEGs[i]),"_Top500_Down.txt"))
}
system(paste0("cat ",projectId,'_',names(degs$listDEGs[i]),"_Top500_Up.txt |sort | uniq | ./l2p >",projectId,'_',names(degs$listDEGs[i]),"_Pathways_Up.txt"))
system(paste0("cat ",projectId,'_',names(degs$listDEGs[i]),"_Top500_Down.txt |sort | uniq | ./l2p >",projectId,'_',names(degs$listDEGs[i]),"_Pathways_Down.txt"))
system(paste0("cat ",'_',names(degs$listDEGs[i]),"_Top500_Up.txt |sort | uniq | ./l2p >",'_',names(degs$listDEGs[i]),"_Pathways_Up.txt"))
system(paste0("cat ",'_',names(degs$listDEGs[i]),"_Top500_Down.txt |sort | uniq | ./l2p >",'_',names(degs$listDEGs[i]),"_Pathways_Down.txt"))

addUpCol = read.delim(paste0(projectId,'_',names(degs$listDEGs[i]),"_Pathways_Up.txt"), sep = '\t')
addDwCol = read.delim(paste0(projectId,'_',names(degs$listDEGs[i]),"_Pathways_Down.txt"), sep = '\t')
addUpCol = read.delim(paste0('_',names(degs$listDEGs[i]),"_Pathways_Up.txt"), sep = '\t')
addDwCol = read.delim(paste0('_',names(degs$listDEGs[i]),"_Pathways_Down.txt"), sep = '\t')

colnames(addUpCol)=c("pval","fdr","ratio","nb.hits","nb.genes.path","nb.user.genes","tot.back.genes","path_id","source","description","type","gene.list")
colnames(addDwCol)=c("pval","fdr","ratio","nb.hits","nb.genes.path","nb.user.genes","tot.back.genes","path_id","source","description","type","gene.list")
addUpCol = addUpCol[order(addUpCol$pval),]
addDwCol = addDwCol[order(addDwCol$pval),]
addUpCol = addUpCol[,c(8,9,10,11,1,2,3,12,4,5,6,7)]
addDwCol = addDwCol[,c(8,9,10,11,1,2,3,12,4,5,6,7)]
write.table(addUpCol, file = paste0(projectId,'_',names(degs$listDEGs[i]),"_Pathways_Up.txt"), sep = '\t', row.names = F)
write.table(addDwCol, file = paste0(projectId,'_',names(degs$listDEGs[i]),"_Pathways_Down.txt"), sep = '\t', row.names = F)
write.table(addUpCol, file = paste0('_',names(degs$listDEGs[i]),"_Pathways_Up.txt"), sep = '\t', row.names = F)
write.table(addDwCol, file = paste0('_',names(degs$listDEGs[i]),"_Pathways_Down.txt"), sep = '\t', row.names = F)
up_down[[1]]=addUpCol
up_down[[2]]=addDwCol
names(up_down) = c("upregulated_pathways","downregulated_pathways")
Expand Down Expand Up @@ -438,7 +438,7 @@ ss = function(deg_normAnnot, species, geneSet) {
}
gset = getGmt(getSet)
ssgsResults = gsva(ssgs, gset, method='ssgsea') #run ssGSEA
y<-paste("_",projectId, sep="") #write out results
y<-paste("_", sep="") #write out results
tSS = tempfile(pattern = "ssGSEA_enrichmentScores_", tmpdir = getwd(), fileext = paste0(y,'.txt'))
write.table(ssgsResults,file=tSS,sep="\t",col.names=NA)
myfactor <- factor(deg_normAnnot$pheno$groups)
Expand All @@ -455,7 +455,7 @@ ss = function(deg_normAnnot, species, geneSet) {
all.pathways = topTable(ebayes.fit2, coef=i, number=nrow(ebayes.fit2)) #Determine DE pathways
all.pathways = all.pathways[order(abs(all.pathways$P.Value)),]
colnames(all.pathways)[2] = 'Avg.Enrichment.Score'
write.table(all.pathways,file=paste0(projectId,"_",cons[i],"_ssGSEA_pathways.txt"),sep="\t",row.names=T,col.names=NA)
write.table(all.pathways,file=paste0("_",cons[i],"_ssGSEA_pathways.txt"),sep="\t",row.names=T,col.names=NA)
DEss[[i]] = all.pathways
}
names(DEss)=cons
Expand Down

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