scaleScoreMatrix-methods: Scales the values in the matrix by rows and/or columns

In genomation: Summary, annotation and visualization of genomic data

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)

genomation documentation built on Nov. 8, 2020, 5:21 p.m.