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 1.18.1 Index]