enrichmentMatrix {genomation} | R Documentation

## Compute an enrichment of IP over control both stored in ScoreMatrix objects

### 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)

[Package genomation version 1.11.3 Index]