RepeatMaskerGR: extract GRanges object corresponding to RepeatMasker...

In sagrudd/nanopoRe: Accessory Methods for the Analysis of Oxford Nanopore Technologies DNA Sequence Data

Description

this method is used to extract most salient data from the RepeatMasker annotation file into a GRanges object so that Genome Geometry analyses can be performed and genome coordinates can be used to quickly associate with repeat types

Usage

RepeatMaskerGR(RepeatMaskerFile = NULL, RepeatMaskerSRC = NULL,
    force = FALSE)

Arguments

RepeatMaskerFile	is a path to an already downloaded RepeatMasker results file
RepeatMaskerSRC	is the URL to RepeatMasker dataset
force	is a boolean to specify whether the build of external data should be forced

Value

GRanges object of annotated repeats

Examples

# Using C.elegans repeats as demo; small file with only 90k repeats = easy
src <- paste0("http://www.repeatmasker.org/genomes/ce10/",
    "RepeatMasker-rm405-db20140131/ce10.fa.out.gz")
# if you roll your eyes and sigh - then please feel my frustration with the
# required strict adherence to Bioc conventions for line length ...
repeats <- RepeatMaskerGR(RepeatMaskerSRC=src)

sagrudd/nanopoRe documentation built on June 7, 2020, 10:20 p.m.