read.rmskFasta {CNEr}R Documentation

Read a soft repeat masked fasta

Description

Read a soft repeat masked fasta file into a GRanges object.

Usage

  read.rmskFasta(fn)

Arguments

fn

character(1): The filename of the soft repeat masked fasta.

Details

Only the lower case based ("a", "c", "g", "t") are considered in the soft repeat masked fasta.

Value

GRanges object with coordinates of repeat masked regions.

Author(s)

Ge Tan

See Also

read.rmMask.GRanges

Examples

  fn <- file.path(system.file("extdata", package="CNEr"),
                  "rmsk.fa")
  read.rmskFasta(fn)
[Package CNEr version 1.24.0 Index]