scaleScoreMatrix {genomation} | R Documentation

## Scales the values in the matrix by rows and/or columns

### Description

Scales the values in the matrix by rows and/or columns

### Usage

    scaleScoreMatrix(mat, columns = FALSE, rows = TRUE, scalefun = NULL)

    ## S4 method for signature 'ScoreMatrix'
    scaleScoreMatrix(mat, columns = FALSE, rows = TRUE,
      scalefun = NULL)

### Arguments

`mat` | `ScoreMatrix` object
`columns` | `columns` whether to scale the matrix by columns. Set by default to FALSE.
`rows` | `rows` Whether to scale the matrix by rows. Set by default to TRUE
`scalefun` | function object that takes as input a matrix and returns a matrix. By default the argument is set to (x - mean(x))/(max(x)-min(x)+1)

### Value

`ScoreMatrix` object

### Examples

    # scale the rows of a scoreMatrix object
    library(GenomicRanges)
    target = GRanges(rep(c(1,2),each=7), IRanges(rep(c(1,1,2,3,7,8,9), times=2), width=5),
             weight = rep(c(1,2),each=7),
             strand=c('-', '-', '-', '-', '+', '-', '+', '-', '-', '-', '-', '-', '-', '+'))
    windows = GRanges(rep(c(1,2),each=2), IRanges(rep(c(1,2), times=2), width=5),
               strand=c('-','+','-','+'))
    sm = ScoreMatrix(target, windows)
    ssm = scaleScoreMatrix(sm, rows=TRUE)

[Package genomation version 1.20.0 Index]