rank_rbm: rank_rbm() This function subsets the provided methylRaw...

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

Description

rank_rbm() This function subsets the provided methylRaw objects by the specified GRange and returns a list of dataframes containing the GRange regions ranked by methylation site density.

Usage

rank_rbm(
  mrobjscd,
  mrobjhsm,
  region.gr,
  rlabel = "",
  minrwidth = 1,
  maxrwidth = 1e+06,
  minnbrsites = 1,
  withglink = "",
  outflabel = ""
)

Arguments

mrobjscd	A methylKit methylRaw or methylRawList object for scd sites
mrobjhsm	A methylKit methylRaw or methylRawList object for hsm sites
region.gr	A GRanges object (typically based on the relevant genome annotation)
rlabel	A string to identify the type of region analyzed
minrwidth	Minimal region width for region to be included in plot
maxrwidth	Maximal region width for region to be included in plot
withglink	Either NCBIgene or "" to indicate inclusion of a gene link column in the output if available
outflabel	A string to identify the output dataframe
minbrsites	Minimal number of methylation sites in region for region to be included in plot

Value

A list of lists of dataframes containing (for each sample) the GRange regions ranked by overall methylation percentage (over all scd sites) or methylation hsm site density

Examples

  mydatf <- system.file("extdata","Am.dat",package="BWASPR")
  myparf <- system.file("extdata","Am.par",package="BWASPR")
  myfiles <- setup_BWASPR(datafile=mydatf,parfile=myparf)
  AmHEscd <- mcalls2mkobj(myfiles$datafiles,species="Am",study="HE",
                          type="CpGscd",mincov=1,assembly="Amel-4.5")
  AmHEhsm <- mcalls2mkobj(myfiles$datafiles,species="Am",study="HE",
                          type="CpGhsm",mincov=1,assembly="Amel-4.5")
  genome_ann <- get_genome_annotation(myfiles$parameters)
  rgL <- rank_rbm(AmHEscd,AmHEhsm,region.gr=genome_ann$gene,rlabel="genes",
                  withglink="NCBIgene",outflabel="Am_HE")

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