Basic4Cseq (version 1.8.0)

printBEDFragmentLibrary: Print a BED-file fragment library

Description

This function extracts the first columns of a virtual fragment library file and exports them as a BED-file for use with other tools (e.g. visualization in the Integrative Genomics Viewer (IGV).)

Usage

printBEDFragmentLibrary(fragmentLibrary, BEDLibraryName, minFragEndLength = 0, zeroBased = FALSE)

Arguments

fragmentLibrary

Virtual fragment library file name

BEDLibraryName

File name for the exported BED file

minFragEndLength

Minimum fragment end length to be considered

zeroBased

If TRUE, adapt the start of the BED-file fragments

Value

Examples

  if(interactive()) {
    file <- system.file("extdata", "vfl_aagctt_catg_mm9_54_vp.csv", package="Basic4Cseq")
    printBEDFragmentLibrary(file, "BEDLibrary_FL_vp.bed")
  }