extracting_modifying_methLabels: Main function to call the extraction, modification and...

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

Description

Main function to call the extraction, modification and quantification process.

Usage

extracting_modifying_methLabels(
  cmaploc_mol,
  untar = FALSE,
  cntNick,
  cntMeth,
  selectedRegion = TRUE,
  chrom,
  startPos,
  endPos,
  outputFormat = c("individualText", "multipleText", "dataFrame"),
  path,
  logFilename
)

Arguments

cmaploc_mol	character. path to the cmap folder.
untar	boolean. untar option. True or False/
cntNick	integer. Nick label value.
cntMeth	integer. Meth label value.
selectedRegion	boolean. if TRUE, selected region is analyzed and the user provides chromosome and start and end point. If FALSE, whole genome analysed.
chrom	character. Chromosome number if selectedRegion is TRUE
startPos	integer. Start of the query if selectedRegion is TRUE
endPos	integer. End of the query if selectedRegion is TRUE
outputFormat	Character. Choices are individualText, multipleText and dataframe.
path	Character. Path of the folder where log files needs to be written to.
logFilename	character. Log file name.

Value

dataframe or text files containing the modified files.

Examples

## Not run: 
molcmap <- system.file("extdata", "SampMolecule.cmap", package="methometR")
cmap <- system.file("extdata", "SampContig.cmap", package="methometR")
bed<-molMethylRefLoc(nickrefLoc,molcmap,xmapdata, contigID, cntNick , 
   cntMeth)

## End(Not run)

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