cmpSamples: cmpSamples() This function will methylKit::unite() input...

In BrendelGroup/BWASPR: Various R functions and scripts for the analyis of BWASP workflow output

Description

cmpSamples() This function will methylKit::unite() input samples and compare them using methylKit::getCorrelation() and methylKit::PCASamples.

Usage

cmpSamples(mrobj, destrand = FALSE, mc.cores = 1, plotfile = "")

Arguments

mrobj	A methylRaw object as returned by methylKit::unite()
destrand	methylKit::unite() parameter; default: FALSE. destrand=TRUE combines CpG methylation calls from both strands.
mc.cores	Integer denoting how many cores should be used for parallel diffential methylation calculations
plotfile	If specified other than the default "", then plots are saved in PDF file "plotfile".pdf; otherwise either no plots are generated or the R default plot outputs are used.

Value

the data obtained from methylKit::unite()

Examples

  mydatf <- system.file("extdata","Am.dat",package="BWASPR")
  myparf <- system.file("extdata","Am.par",package="BWASPR")
  myfiles <- setup_BWASPR(datafile=mydatf,parfile=myparf)
  AmHE <- mcalls2mkobj(myfiles$datafiles,species="Am",study="HE",
                       sample="all",replicate=c(0),
                       type="CpGhsm", mincov=1,
                       assembly="Amel-4.5")
  cmpSamples(AmHE,destrand=TRUE,mc.cores=4,plotfile="myplots")

BrendelGroup/BWASPR documentation built on Feb. 6, 2022, 9:09 a.m.