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

In genomation: Summary, annotation and visualization of genomic data

Description

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

Usage

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

Arguments

IP	ScoreMatrixList object storing IP samples
control	ScoreMatrixList storing control samples

Value

ScoreMatrixList 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

ScoreMatrixList

Examples

#load IP and control BAM files and create ScoreMatrix objects
library('genomationData')
data(promoters)
bam.file_IP_1 <- system.file("extdata", 
"wgEncodeSydhTfbsH1hescZnf143IggrabAlnRep1.chr21.bam", package = "genomationData")
IP_1 <- ScoreMatrix(target = bam.file_IP_1, windows = promoters, type = 'bam')

bam.file_IP_2 <- system.file("extdata", 
"wgEncodeBroadHistoneH1hescSuz12051317AlnRep1.chr21.bam", package = "genomationData")
IP_2 <- ScoreMatrix(target=bam.file_IP_2, windows = promoters, type = 'bam')

bam.file_c <- system.file("extdata", 
"wgEncodeBroadHistoneH1hescCtcfStdAlnRep1.chr21.bam", package = "genomationData")
control <- ScoreMatrix(target = bam.file_c, windows = promoters, type = 'bam')

# create a ScoreMatrixList object storing IP ScoreMatrix objects
sml_IP <- ScoreMatrixList(list(IP1 = IP_1, IP2 = IP_2))

# create a ScoreMatrixList object storing control ScoreMatrix objects
sml_control <- ScoreMatrixList(list(c1 = control, c2 = control))

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

genomation documentation built on Nov. 8, 2020, 5:21 p.m.