cmpSites: cmpSites() This function compares (potential) methylation...

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

Description

cmpSites() This function compares (potential) methylation sites between two samples.

Usage

cmpSites(
  sample1hsm,
  sample1scd,
  sample1label,
  sample2hsm,
  sample2scd,
  sample2label,
  nbrpms,
  plotfile,
  covlist,
  hheight,
  nbrpnts = 5000
)

Arguments

sample1hsm	A methylRaw object for hsm sites of sample 1.
sample1scd	A methylRaw object for scd sites of sample 1.
sample1label	A string serving as a label for sample 1.
sample2hsm	A methylRaw object for hsm sites of sample 2.
sample2scd	A methylRaw object for scd sites of stample 2.
sample2label	A string serving as a label for sample 2.
nbrpms	Integer representing the number of potential methylation sites in the genome; typically derived from the input *.par file.
plotfile	If specified other than the default "", then plots are saved in PDF file "plotfile".pdf; otherwise no plots are generated.
covlist	A vector listing the coverage (number of reads) values to be explored; e.g., c(6,8,10) would compare sites with minimum coverage 6, 8, and 10, successively
hheight	Histogram height for methylation level plot; default: 0.10
nbrpnts	Number of common sites to be sampled for the methylation levels scatter plot; default: 5000

Value

A list of data frames containing data on unique and common sites comparing the two samples.

Examples

  mydatf <- system.file("extdata","Am.dat",package="BWASPR")
  myparf <- system.file("extdata","Am.par",package="BWASPR")
  myfiles <- setup_BWASPR(datafile=mydatf,parfile=myparf)
  nbrpms  <- as.numeric(myfiles$parameters[
    myfiles$parameters$Variable == "TOTALNBRPMSITES",2])
  AmHEhsm <- mcalls2mkobj(myfiles$datafiles,species="Am",study="HE",
                          type="CpGhsm", mincov=1,assembly="Amel-4.5")
  AmHEscd <- mcalls2mkobj(myfiles$datafiles,species="Am",study="HE",
                          type="CpGscd", mincov=1,assembly="Amel-4.5")
  s1hsm <- methylKit::getData(AmHEhsm[[1]])
  s1scd <- methylKit::getData(AmHEscd[[1]])
  s2hsm <- methylKit::getData(AmHEhsm[[2]])
  s2scd <- methylKit::getData(AmHEscd[[2]])
  mydflist <- cmpSites(s1hsm,s1scd,"Am_HE_fr",s2hsm,s2scd,"Am_HE_rn",nbrpms,
                       plotfile="pwc.pdf",covlist=c(6,10,20),hheight=0.10,
                       nbrpnts=5000)

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