Import TE intervals from UCSC table browser

Import TE intervals from UCSC table browser

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