scaleScoreMatrixList {genomation} | R Documentation

## Scale the ScoreMatrixList

### Description

Scales each ScoreMatrix in the ScoreMatrixList object, by rows and/or columns

### Usage

    scaleScoreMatrixList(sml, columns, rows, scalefun)

    ## S4 method for signature 'ScoreMatrixList'
    scaleScoreMatrixList(sml, columns = FALSE,
      rows = TRUE, scalefun = NULL)

### Arguments

`sml` | a `ScoreMatrixList` object
`columns` | a `columns` whether to scale the matrix by columns. Set by default to FALSE
`rows` | a `rows` Whether to scale the matrix by rows. Set by default to TRUE
`scalefun` | a function object that takes as input a matrix and returns a matrix. By default the argument is set to the R scale function with center=TRUE and scale=TRUE

### Value

`ScoreMatrixList` object

### Examples

    library(GenomicRanges)
    data(cage)
    data(cpgi)
    data(promoters)

    cage$tpm = NULL
    targets = GRangesList(cage=cage, cpgi=cpgi)
    sml = ScoreMatrixList(targets, promoters, bin.num=10, strand.aware=TRUE)
    sml.scaled = scaleScoreMatrixList(sml, rows=TRUE)
    sml.scaled

    multiHeatMatrix(sml)

[Package genomation version 1.12.0 Index]