cmStats: cmStats() This function generates coverage and methylation...

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

cmStats() This function generates coverage and methylation statistics for the input data set.

Description

cmStats() This function generates coverage and methylation statistics for the input data set.

Usage

cmStats(
  mrobj,
  type = "CpGhsm",
  covlist = c(10),
  locount = 100,
  hicount = 1000,
  outfile = "",
  plotfile = ""
)

Arguments

mrobj	A methylRaw object
type	The type should be CpGhsm or CpGscd, as per BWASP output.
covlist	A vector of coverage threshols; default: c(10)
locount	Low coverage threshold for statistics on a range of sites; default: c(100)
hicount	High coverage threshold for statistics on a range of sites; default: c(1000)
outfile	If specified then output is printed to the specified file.
plotfile	If specified other than the default "", then plots are saved in PDF file "plotfile".pdf; otherwise either no plots are generated or the R default plot outputs are used.

Value

the coverage count for the highest threshold in covlist

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")
  cmStats(AmHE[[1]],type="CpGhsm",covlist=c(10,20),locount=100,hicount=1000,
          outfile="Am_HE-statistics.txt",plotfile="myplots")

BrendelGroup/BWASPR documentation built on June 2, 2025, 7:25 a.m.