importUCSC: Import TE intervals in UCSC table browser format

Description Usage Arguments Value

View source: R/import.R

Description

Import TE intervals from UCSC table browser

Usage

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importUCSC(path = "path to UCSC RMSK file", curate = FALSE,
  main_classes = TRUE, main_assembly = TRUE)

Arguments

path

Character. Path to file.

curate

Logical. If TRUE, calls 'curateTEs' to resolve overlapping TE intervals.

main_classes

Logical. If TRUE (the default), only returns TE intervals unambiguously belonging to DNA, LINE, SINE, and LTR classes.

main_assembly

Logical. If TRUE (the default), only returns TE intervals on the main chromosomes.

Value

Returns a GRanges object with TE intervals


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