Description Usage Arguments Examples
ProcessOutputFilesFromDoGsOnly
1 2 3 4 | ProcessOutputFilesFromDoGsOnly(dir.name, input.file.pattern, out.dir.name,
out.file.pattern.interested, out.file.pattern.positive.gene,
out.file.pattern.negative.gene, out.file.pattern.all, dir.name.gene.list,
pattern.4.gene.list, adjust_by_batch, permutation.set.up = NULL)
|
adjust_by_batch |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 | dir.name='/media/aiminyan/DATA/Ramin_azhang/Counts4DoGsOnlyRmOne/'
input.file.pattern='*count.2.txt'
dir.name.gene.list='/media/H_driver/2016/Ramin_azhang/'
pattern.4.gene.list='final_list.csv'
out.dir.name='/media/aiminyan/DATA/Ramin_azhang/Counts4DoGsOnlyRmOne/'
for (i in 1:10) {
time.string = gsub(':', '-', gsub(' ', '_', as.character(Sys.time())))
out.dir.name=paste0('/media/aiminyan/DATA/Ramin_azhang/Counts4DoGsOnlyRmOnePermutationAt_',time.string,'/')
dir.create(out.dir.name)
out.file.pattern.interested='DoGs_adjust_by_batch_interested_gene'
out.file.pattern.positive.gene='DoGs_adjust_by_batch_positive'
out.file.pattern.negative.gene='DoGs_adjust_by_batch_negative'
out.file.pattern.all= 'DoGs_adjust_by_batch_all'
Re.unadjusted.adjusted<-ProcessOutputFilesFromDoGsOnly(dir.name,input.file.pattern,out.dir.name,out.file.pattern.interested,
out.file.pattern.positive.gene,
out.file.pattern.negative.gene,
out.file.pattern.all,
dir.name.gene.list,
pattern.4.gene.list,
adjust_by_batch='YES')
}
save.image(file=paste0(out.dir.name,'re_save_2.RData'))
savehistory(file=paste0(out.dir.name,'re_save_2.Rhistory'))
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