enrichmentMatrix,ScoreMatrixList,ScoreMatrixList-method {genomation} | R Documentation

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

### 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)

[Package genomation version 1.20.0 Index]