det_dmt: det_dmt() This function generates list of differentially...

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

Description

det_dmt() This function generates list of differentially methylated CpG tiles and the corresponding genes, as determined by application of methylKit functions.

Usage

det_dmt(
  mrobj,
  genome_ann,
  wsize = 1000,
  stepsize = 1000,
  threshold = 25,
  qvalue = 0.01,
  mc.cores = 1,
  destrand = FALSE,
  outfile1 = "dmt.txt",
  outfile2 = "dmg.txt"
)

Arguments

mrobj	A methylKit methylRaw or methylRawList object
genome_ann	Genome annotation returned by get_genome_annotation()
wsize	The window size for the sliding windows (tiles), default wsize = 1000
stepsize	The step size for the sliding window starts, default stepsize = 1000
threshold	Cutoff for percent methylation difference, default threshold = 25.0
qvalue	Cutoff for q-value, default q-value = 0.01
mc.cores	Integer denoting how many cores should be used for parallel diffential methylation calculations
destrand	methylKit::unite() parameter; default: FALSE. destrand=TRUE combines CpG methylation calls from both strands.
outfile1	File name to which differentially methylated tiles are written
outfile2	File name to which differentially methylated genes are written

Value

A Granges object that contains a list of genes that have diff methylated C tiles

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$datafiles,species="Am",study="HE",type="CpGscd",
                       mincov=1,assembly="Amel-4.5")
  genome_ann <- get_genome_annotation(myfiles$parameters)
  mTlist <- det_dmt(AmHE,genome_ann,threshold=25.0,qvalue=0.01,mc.cores=4,
                    outfile1="AmHE-dmtiles.txt", 
                    outfile2="AmHE-dmgenes.txt") 

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