molNickLoc: Mapping nick label location from contig to molecule

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

Description

Mapping nick label location from contig to molecule

Usage

molNickLoc(nickrefLoc, molcmap, xmapdata, contigID, cntNick, cntMeth)

Arguments

nickrefLoc	character. Path to Bionano compressed file.
molcmap	character. molecule cmap data.
xmapdata	character. contig-molecule xmap data.
contigID	character. query contig ID.
cntNick	integer. Nick label value.
cntMeth	integer. Meth label value.

Value

dataframe containing the molecule file, with the nick position

Examples

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
modxmap <- readingXmap(xmap)
cmap <- system.file("extdata", "Cmapdir/output/contigs/exp_refineFinal1/merged_smaps/SampMolecule_q.cmap", package="methometR")
modcmap <- readingCmap(cmap) 
modMolcmap <- modmolcmap(molcmap = modcmap,
  xmapdata = modxmap,
  cntNick = 1,
  cntMeth=2)
contigmodcmap <- readingXmap(contigcmap)
modmolcmapNick <-molNickLoc(nickrefLoc = nickRef,
   molcmap = modMolcmap,
   xmapdata = modxmap, 
   contigID = contigID, cntNick = cntNick, 
   cntMeth = cntMeth)

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