Import TE intervals from Repeatmasker

Imports TE interval coordinates from Repeatmasker

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