importRMSK: Import TE intervals in Repeatmasker format

In tanaylab/reputils: Utility functions for working with transposable elements

Description

Imports TE interval coordinates from Repeatmasker

Usage

importRMSK(path, curate = FALSE, main_assembly = TRUE,
  main_classes = TRUE, proper_alignments = TRUE)

Arguments

path	Character. Path to file.
curate	Logical. If TRUE, calls 'curateTEs' to resolve overlapping TE intervals.
main_assembly	Logical. If TRUE (the default), only returns TE intervals on the main chromosomes.
main_classes	Logical. If TRUE (the default), only returns TE intervals unambiguously belonging to DNA, LINE, SINE, and LTR classes.
proper_alignments	Logical. If TRUE (the default), only returns TE intervals with proper start and end coordinates.

Value

Returns a GRanges object with TE intervals

tanaylab/reputils documentation built on Nov. 5, 2019, 9:58 a.m.