AnntationUsingChipSeeker: AnntationUsingChipSeeker

In aiminy/ChipSeq: An R Package for Performing ChipSeq Analysis In One Step

Description

Use ChipSeeker to annotate data

Usage

AnntationUsingChipSeeker(dir.name, input.file.pattern, out.dir.name,
  txdb = c("hg19", "hg38"), DD, distanceToTSS_cutoff = 5000,
  assignGenomicAnnotation = TRUE, AP = c("Promoter", "5UTR", "3UTR", "Exon",
  "Intron", "Downstream", "Intergenic"))

Arguments

input.file.pattern	: input file pattern
out.dir.name	output file directory
txdb	Annotation databased to be used("hg19","hg38")
DD	distance definition around TSS
dir.name:	path for bed files

Examples

dir.name="/Volumes/Bioinformatics$/2017/DannyNewData/BindDiff/common_peaks_bed"
input.file.pattern="common_peaks.bed"
out.dir.name="/Volumes/Bioinformatics$/2017/DannyNewData/AnnotationNew"
txdb="hg19"
DD=5000

AnntationUsingChipSeeker(dir.name,input.file.pattern,out.dir.name,txdb=txdb,DD,distanceToTSS_cutoff=5000, AP=c("Promoter","Intron"))

AnntationUsingChipSeeker(dir.name,input.file.pattern,out.dir.name,txdb=txdb,DD,distanceToTSS_cutoff=5000,AP=c("Promoter"))

AnntationUsingChipSeeker(dir.name,input.file.pattern,out.dir.name,txdb=txdb,DD,distanceToTSS_cutoff=5000,AP=c("Intron"))
  

aiminy/ChipSeq documentation built on May 12, 2019, 3:37 a.m.