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

Description Usage Arguments Value Examples

Description

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

Usage

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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

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# 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)

BIMSBbioinfo/genomation documentation built on Feb. 4, 2018, 12:11 p.m.