ProcessOutputFilesFrom5Cases: ProcessOutputFilesFrom5Cases

In aiminy/3UTR-Seq: An R package for processing and analyzing 3UTR,DOGs and 5UTR data

Description

read the mapping results from the Dogs of each gene

Usage

ProcessOutputFilesFrom5Cases(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)

Arguments

dir.name:	the path for input files
input.file.pattern:	input file pattern

Examples

dir.name="/media/aiminyan/DATA/Ramin_azhang/Counts5CasesEachSample/"
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/Counts5CasesEachSample/"

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<-ProcessOutputFilesFrom5Cases(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"))

aiminy/3UTR-Seq documentation built on May 10, 2019, 7:36 a.m.