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

Usage

map_mrpr(hsmrL, species, slabel, genome_ann, gnmsize, UTRflag, outfile)

Arguments

hsmrL	List of data frames with hsm rich and poor regions, as put out by
species	Label for the species being analyzed
slabel	Label for the sample
genome_ann	A list of GRanges objects that contains genome annotation.
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

Data frames describing genes overlapping with methylation-rich and poor regions

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$Variable == "UTRFLAGSET",2])
  AmHE <- mcalls2mkobj(infiles$datafiles,species="Am",study="HE",
                       sample=list("forager","nurse"),replicate=c(0),
                       type="CpGhsm",mincov=1,assembly=asmblv
                      )
  hsmrL <- det_mrpr(AmHE[[1]],"Am_HE_fr",ddset=c(1,5),outfile="dst-Am_HE_fr.txt",nr2d=10L,doplots=TRUE)
  ginfo <- get_genome_annotation(infiles$parameters)
  map_mrpr(hsmrL,species="Am",slabel="forager_hsm",ginfo,gnmsize,UTRflag=UTRflag,
           outfile="AmHE-region.map.txt"
          )

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