GenerateBins: generate genome-wide bins for counting purpose

In stjude/ChIPseqSpikeInFree: A Spike-in Free ChIP-Seq Normalization Approach for Detecting Global Changes in Histone Modifications

generate genome-wide bins for counting purpose

Description

Given a chrom.size file, this function allows you to generate a your own sliding windows (bins).

Usage

GenerateBins(chromFile, binSize = 1000, overlap = 0, withChr = TRUE)

Arguments

chromFile	chrom.size. Given "hg19","mm10","mm9" or "hg38", will load chrom.size file from package folder.
binSize	size of bins (bp)
overlap	overlaps between two consecutive bins (bp)
withChr	chromosome names in bin File have chr if set withChr to TRUE; FALSE - no chr

Value

A data.frame of generated bins

Examples

## 1. generate a mm10 binFile without chr and use a binSize of 1000 bp
## and overlap of 500 bp between two consecutive bins

## "mm10" will be parsed as system.file("extdata", "mm10.chrom.sizes",
##       package = "ChIPseqSpikeInFree")
# binDF <- GenerateBins(chromFile="mm10",binSize=1000, overlap=500,
# withChr=FALSE,prefix="mm10")

## 2. generate a hg19 binFile with chr and use a binSize of 2000 bp

## "hg19" will be parsed as system.file("extdata", "hg19.chrom.sizes",
##       package = "ChIPseqSpikeInFree")
# binDF<- GenerateBins(chromFile="hg19",binSize=2000, overlap=0,
# withChr=TRUE,prefix="hg19")

stjude/ChIPseqSpikeInFree documentation built on March 28, 2022, 5:36 a.m.