explore_dmsg: explore_dmsg() This function sorts genes by meth_level per...

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

Description

explore_dmsg() This function sorts genes by meth_level per 10kb for individual samples and sorts genes by meth_diff per 10kb for each comparison; sample percent methylation per site values are compared with the Wilcoxon signed rank test

Usage

explore_dmsg(
  mrobj,
  genome_ann,
  dmgprp,
  maxgwidth,
  minnbrdmsites,
  withglink = "NCBIgene",
  outflabel = ""
)

Arguments

mrobj	A methylKit methylRaw or methylRawList object
genome_ann	Genome annotation returned by get_genome_annotation()
dmgprp	A list of data frames containing dmsg data generated by show_dmsg()
maxgwidth	An integer specifying the maximum gene width for a gene to be listed in the output tables [default: -1, interpreted to mean no restriction]
minnbrdmsites	An integer specifying the minimum number of differentially methylated sites for a gene to be listed in the pairwise sample comparisons [default: 1]
withglink	Either NCBIgene or "" to indicate inclusion of a gene link column in the output
outflabel	A string to identify the study in the output file

Value

A list of data frames summarizing single sample and pairwise comparison gene properties

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$datafiles,species="Am",study="HE",
                       type="CpGhsm",mincov=1,assembly="Amel-4.5")
  genome_ann <- get_genome_annotation(myfiles$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,min.nsites=10,destrand=TRUE,
                      outflabel="Am_HE")
  summaries <- explore_dmsg(AmHE,genome_ann,dmgprp,maxgwidth=20000,
                            minnbrdmsites=2, withglink="NCBIgene",
                            outflabel="Am_HE")

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