enrichmentMatrix-ScoreMatrix-method: Compute an enrichment of IP over control both stored in...

In BIMSBbioinfo/genomation: Summary, annotation and visualization of genomic data

Description

This is an enrichmentMatrix function for ScoreMatrix objects, that enables to normalize ChIP-seq signals with respect to IgG or input DNA control.

Usage

\S4method{enrichmentMatrix}{ScoreMatrix,ScoreMatrix}(IP, control)

Arguments

IP	ScoreMatrix object storing an IP sample
control	ScoreMatrix object storing a control sample

Value

ScoreMatrix object

Note

The function computes an enrichment of IP over control as follow: Suppose both IP and control are ScoreMatrix objects that have same dimensions. Then, the enrichment is calculated usign a formula: log2((IP + 1) / (control + 1)).

See Also

ScoreMatrix

Examples

 
#load IP and control BAM files and create ScoreMatrix objects
library('genomationData')
bam.file_IP <- system.file("extdata", 
"wgEncodeBroadHistoneH1hescSuz12051317AlnRep1.chr21.bam", package = "genomationData")
bam.file_c <- system.file("extdata", 
"wgEncodeBroadHistoneH1hescCtcfStdAlnRep1.chr21.bam", package = "genomationData")
data(promoters)
IP <- ScoreMatrix(target = bam.file_IP, windows = promoters, type = 'bam')
control <- ScoreMatrix(target = bam.file_c, windows = promoters, type = 'bam')

# compute an enrichment of IP over control
enrichmentMatrix(IP, control)

BIMSBbioinfo/genomation documentation built on March 13, 2020, 5:28 a.m.