enrichmentMatrix,ScoreMatrixList,ScoreMatrix-method {genomation} | R Documentation |
This is an enrichmentMatrix
function for IP ScoreMatrixList
object and control ScoreMatrix
object,
that enables to normalize ChIP-seq signals with respect to IgG or input DNA control.
\S4method{enrichmentMatrix}{ScoreMatrixList,ScoreMatrix}(IP, control)
IP |
|
control |
|
ScoreMatrixList
object
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)).
#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)) # compute an enrichment of IP over control enrichmentMatrix(sml_IP, control)