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

Usage

1

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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
#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)

BIMSBbioinfo/genomation documentation built on Feb. 4, 2018, 12:11 p.m.