read.rmMask.GRanges {CNEr}R Documentation

Read a RepeatMasker .out file

Description

Read a RepeatMasker .out file into a GRanges object.

Usage

  read.rmMask.GRanges(fn)

Arguments

fn

character(1): the filename of a RepeatMasker .out file.

Value

A GRanges object with metadata columns containing the name of the matching interspersed repeat, the class of the repeat and the Smith-Waterman score of the match.

Author(s)

Ge Tan

References

http://www.repeatmasker.org/webrepeatmaskerhelp.html

Examples

  fn <- system.file("extdata", "ce2chrM.fa.out", package="IRanges")
  read.rmMask.GRanges(fn)

[Package CNEr version 1.28.0 Index]