fetchRMSK {REMP}R Documentation

Get RE database from RepeatMasker

Description

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

Usage

fetchRMSK(ah, REtype, verbose = FALSE)

Arguments

ah

An AnnotationHub object. Use AnnotationHub() to retrive information about all records in the hub.

REtype

Type of RE. Currently "Alu" and "L1" are supported.

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

ah <- AnnotationHub::AnnotationHub()
L1 <- fetchRMSK(ah, 'L1', verbose = TRUE)
L1


[Package REMP version 1.4.1 Index]