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

View source: R/cmpSites.R

cmpSitesR Documentation

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

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 June 2, 2025, 7:25 a.m.