show_dmsg: show_dmsg() This function generates will plot heatmaps of...

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

Description

show_dmsg() This function generates will plot heatmaps of methylation level of sites in dmgenes

Usage

show_dmsg(
  mrobj,
  dmsg,
  destrand = FALSE,
  min.nsites = 2,
  max.nsites = 60,
  min.pdmsites = 10,
  mc.cores = 1,
  outflabel = ""
)

Arguments

mrobj	A methylKit methylRaw or methylRawList object
dmsg	A list containing GRanges objects dmsites and dmgenes returned by det_dmsg()
destrand	methylKit::unite() parameter; default: FALSE. destrand=TRUE combines CpG methylation calls from both strands
min.nsites	Required minimal number of msites in a gene for the gene to be displayed in the heatmap pdf
max.nsites	Required maximal number of msites in a gene for the gene to be displayed in the heatmap pdf
min.pdmsites	Required minimal percent of dmsites among the msites in a gene for the gene to be displayed in the heatmap pdf
mc.cores	Integer denoting how many cores should be used for parallel diffential methylation calculations
outflabel	A string to identify the study in the output file

Value

A data frame

Examples

  mydatf <- system.file("extdata","Am.dat",package="BWASPR")
  myparf <- system.file("extdata","Am.par",package="BWASPR")
  myfiles <- setup_BWASPR(datafile=mydatf,parfile=myparf)
  samplelist <- list("forager","nurse")
  AmHE <- mcalls2mkobj(myfiles$datafiles,species="Am",study="HE",
                       sample=samplelist,replicate=c(0),
                       type="CpGhsm",mincov=1,assembly="Amel-4.5")
  genome_ann <- get_genome_annotation(myfiles$parameters)
  dmsgList <- det_dmsg(AmHE,genome_ann,
                       threshold=25.0,qvalue=0.01,mc.cores=4,destrand=TRUE,
                       outfile1="AmHE-dmsites.txt", 
                       outfile2="AmHE-dmgenes.txt")
  dmgprp <- show_dmsg(AmHE,dmsgList,destrand=TRUE,
                      min.nsites=2,max.nsites=60,min.pdmsites=10,
                      mc.cores=4,outflabel="Am_HE")

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