liftCoords: Run liftover to convert coordinates from one genome version...

In sherrillmix/dnar: Miscellaneous functions to deal with bioinformatic analyses

Run liftover to convert coordinates from one genome version to another

Description

Run liftover to convert coordinates from one genome version to another

Usage

liftCoords(
  chr,
  start,
  end,
  strand,
  chainFile,
  liftoverBin = "liftOver",
  vocal = FALSE,
  removeNAs = TRUE
)

Arguments

chr	vector of chromosomes
start	vector of start coordinate 1-based
end	vector of end coordinate 1-based
strand	vector of strands
chainFile	location of chain file for liftover
liftoverBin	location of the liftOver executable
vocal	if TRUE then message extra information
removeNAs	if TRUE then remove positions that did could not be lifted over

Value

four column data frame of chr, start, end and strand of coordinates

sherrillmix/dnar documentation built on July 18, 2022, 10:07 p.m.