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Last data update: 2014.03.03

R: Scale the ScoreMatrixList

scaleScoreMatrixList

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)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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> library(genomation)
Loading required package: grid
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/genomation/scaleScoreMatrixList.Rd_%03d_medium.png", width=480, height=480)
> ### Name: scaleScoreMatrixList
> ### Title: Scale the ScoreMatrixList
> ### Aliases: scaleScoreMatrixList
> ###   scaleScoreMatrixList,ScoreMatrixList-method
> 
> ### ** Examples
> 
> library(GenomicRanges)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomeInfoDb
> 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)
working on cage
working on cpgi
> sml.scaled = scaleScoreMatrixList(sml, rows=TRUE)
> sml.scaled
scoreMatrixlist of length:2

1. scoreMatrix with dims: 1055 10
2. scoreMatrix with dims: 1055 10
> ## No test: 
> multiHeatMatrix(sml)
> ## End(No test)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>