fetchRMSK: Get RE database from RepeatMasker

In REMP: Repetitive Element Methylation Prediction

Description

fetchRMSK is used to obtain specified RE database from RepeatMasker Database provided by AnnotationHub.

Usage

fetchRMSK(
  REtype = c("Alu", "L1", "LTR"),
  annotation.source = c("AH", "UCSC"),
  genome = c("hg19", "hg38"),
  verbose = FALSE
)

Arguments

REtype	Type of RE. Currently "Alu", "L1", and "LTR" are supported.
annotation.source	Character parameter. Specify the source of annotation databases, including the RefSeq Gene annotation database and RepeatMasker annotation database. If "AH", the database will be obtained from the AnnotationHub package. If "UCSC", the database will be downloaded from the UCSC website http://hgdownload.cse.ucsc.edu/goldenpath. The corresponding build ("hg19" or "hg38") will be specified in the parameter genome.
genome	Character parameter. Specify the build of human genome. Can be either "hg19" or "hg38".
verbose	Logical parameter. Should the function be verbose?

Value

A GRanges object containing RE database. 'name' column indicates the RE subfamily; 'score' column indicates the SW score; 'Index' is an internal index for RE to facilitate data referral, which is meaningless for external use.

Examples

L1 <- fetchRMSK(REtype = "L1", 
                annotation.source = "AH",
                genome = "hg19", 
                verbose = TRUE)
L1

REMP documentation built on Nov. 8, 2020, 8:05 p.m.