molMethylLoc: Liftover of molecule methylation and nick label position to...

In VilainLab/methometR: methometR: Extracting methylation information from Optical Genome Maps

Description

Liftover of molecule methylation and nick label position to contig coordinates

Usage

molMethylLoc(molcmap, outputType = c("dataframe", "text"), cntMeth, cntNick)

Arguments

molcmap	character. molecule cmap data.
outputType	character. Output method. dataframe or text.
cntMeth	integer. Meth label value.
cntNick	integer. Nick label value.

Value

dataframe containing the molecule file, with the reference position

Examples

xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
cmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
modcmap <- readingCmap(cmap)
modxmap <- readingXmap(xmap)
modMolcmap <- modmolcmap(molcmap = modcmap,
  xmapdata = modxmap,
  cntNick = 1,
  cntMeth=2)
refcontigXmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/ContigRef.xmap", package="methometR")
refCmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/hg19ref_r.cmap", package="methometR")
Contigqcmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1_sv/merged_smaps/SampContig_q.cmap", package="methometR")
refxmapdat <- readingXmap(refcontigXmap)
refcmapdat <- readingCmap(refCmap)
contigcmapdat <- readingCmap(Contigqcmap)
nickRef<-nickReference(refxmap = refxmapdat, refcmap = refcmapdat, 
    contigcmap = contigcmapdat, contigID = 6701, 
   returnMethod =c("dataFrame"),  chrom = 4)
xmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContigMolecule.xmap", package="methometR")
molcmap <- system.file("extdata",  "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
contigcmap <- system.file("extdata",  "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampContig_r.cmap", package="methometR")
contigID = 6701; cntNick = 1; cntMeth=2
contigmodcmap <- readingXmap(contigcmap)
modmolcmapNick <-molNickLoc(nickrefLoc = nickRef,
   molcmap = modMolcmap,
   xmapdata = modxmap, 
   contigID = contigID, cntNick = cntNick, 
   cntMeth = cntMeth)
MethylContigLoc<-molMethylLoc(molcmap = modmolcmapNick,
   outputType = c("dataframe"),
   cntNick = cntNick, 
   cntMeth = cntMeth)

VilainLab/methometR documentation built on Dec. 18, 2021, 6:17 p.m.