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

Description Usage Arguments Value Note See Also Examples

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

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\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

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#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)

genomation documentation built on Nov. 1, 2018, 2:12 a.m.