fetchRMSK {REMP} | R Documentation |
fetchRMSK
is used to obtain specified RE database from RepeatMasker Database
provided by AnnotationHub.
fetchRMSK( REtype = c("Alu", "L1", "LTR"), annotation.source = c("AH", "UCSC"), genome = c("hg19", "hg38"), verbose = FALSE )
REtype |
Type of RE. Currently |
annotation.source |
Character parameter. Specify the source of annotation databases, including
the RefSeq Gene annotation database and RepeatMasker annotation database. If |
genome |
Character parameter. Specify the build of human genome. Can be either |
verbose |
Logical parameter. Should the function be verbose? |
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.
L1 <- fetchRMSK(REtype = "L1", annotation.source = "AH", genome = "hg19", verbose = TRUE) L1