scaleScoreMatrixList: Scale the ScoreMatrixList

In BIMSBbioinfo/genomation: Summary, annotation and visualization of genomic data

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) 

BIMSBbioinfo/genomation documentation built on March 13, 2020, 5:28 a.m.