rank_dmg: rank_dmg() This function sorts dmgenes by ADMpNucl and plots...

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

Description

rank_dmg() This function sorts dmgenes by ADMpNucl and plots bar graph for demonstration

Usage

rank_dmg(explore_dmsg_summaries, outflabel)

Arguments

explore_dmsg_summaries	A list returned by explore_dmsg()
outflabel	A string to identify the study in the output file

Value

A list of data frames summarizing genes sorted by ADMpNucl

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")
  explore_dmsg_summaries <- explore_dmsg(AmHE,genome_ann,dmgprp,maxgwidth=-1,
                                         minnbrdmsites=1,withglink="NCBIgene",
                                         outflabel="Am_HE")
  rnk_pwcomparison_summaries <- rank_dmg(explore_dmsg_summaries,outflabel="Am_HE")

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