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

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

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 Feb. 6, 2022, 9:09 a.m.