map_methylome: map_methylome() This function maps the scd and hsm sites onto...

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

Description

map_methylome() This function maps the scd and hsm sites onto different genomic features (e.g. genes, exon, promoter, etc.)

Usage

map_methylome(
  studymk,
  slabel,
  studymc,
  clabel,
  genome_ann,
  species,
  gnmsize,
  UTRflag,
  outfile = ""
)

Arguments

studymk	methylRaw object representing an hsm sample
slabel	Label for the sample
studymc	methylRaw object representing the scd control
clabel	Label for the control sample
genome_ann	A list of GRanges objects that contains genome annotation.
species	Label for the species being analyzed
gnmsize	Genome size
UTRflag	Numerical, indicating whether or not the annotation included UTRs (1 or 0)
outfile	If specified, then the result is saved in the specified file name.

Value

Should return something useful

Examples

  mydatf <- system.file("extdata","Am.dat",package="BWASPR")
  myparf <- system.file("extdata","Am.par",package="BWASPR")
  infiles <- setup_BWASPR(datafile=mydatf,parfile=myparf)
  asmblv <- infiles$parameters[infiles$parameters$Variable == "ASSEMBLYVERSION",2]
  gnmsize <- as.numeric(infiles$parameters[infiles$parameters$Variable == "GENOMESIZE",2])
  UTRflag <- as.numeric(infiles$parameters[infiles$parameters$Variable == "UTRFLAGSET",2])
  AmHEhsm <- mcalls2mkobj(infiles$datafiles,species="Am",study="HE",
                          sample=list("forager","nurse"),replicate=c(0),
                          type="CpGhsm",mincov=1,assembly=asmblv
                         )
  AmHEscd <- mcalls2mkobj(infiles$datafiles,species="Am",study="HE",
                          sample=list("forager","nurse"),replicate=c(0),
                          type="CpGscd",mincov=1,assembly=asmblv
                         )
  ginfo <- get_genome_annotation(infiles$parameters)
  map_methylome(AmHEhsm[[1]],"forager_hsm",AmHEscd[[1]],"forager_scd",ginfo,
                species="Am",gnmsize,UTRflag=UTRflag,
                outfile="AmHE-methylome-map.txt"
               )

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