molMethylRefLoc: Liftover of molecule methylation and nick contig position to...

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

Description

Liftover of molecule methylation and nick contig position to reference coordinates

Usage

molMethylRefLoc(
  molcmap,
  outputType = c("dataframe", "text"),
  cntMeth = 1,
  cntNick = 2
)

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 methyl label positions mapped to the reference.

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)
MethylRefLoc<-molMethylRefLoc(molcmap = modmolcmapNick,
   outputType = c("dataframe"),
   cntNick = cntNick, 
   cntMeth = cntMeth)

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