annotate_methylome: annotate_methylome() This function annotates the methylome...

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

Description

annotate_methylome() This function annotates the methylome with different genomic features (e.g. genes, exon, promoter, etc.)

Usage

annotate_methylome(
  mrobj,
  genome_ann,
  destrand = FALSE,
  mc.cores = mc.cores,
  outfile = "methylome_ann.txt"
)

Arguments

mrobj	A methylRawList object that is generated by mcalls2mkobj()
genome_ann	A list of GRanges objects that contain genome annotation.
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
outfile	If specified as other than "", the result is saved in the specified file.

Value

A table that displays site methylation percentages and annotation

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$datafiles)
  genome_ann <- get_genome_annotation(myfiles$parameters)
  annotate_methylome(AmHE,genome_ann,mc.cores=4,
                     outfile="AmHE_methylome_ann.txt")

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