fetchRefSeqGene {REMP} | R Documentation |
fetchRefSeqGene
is used to obtain refSeq gene database provided by AnnotationHub.
fetchRefSeqGene(ah, mainOnly = FALSE, verbose = FALSE)
ah |
An |
mainOnly |
Logical parameter. See details. |
verbose |
Logical parameter. Should the function be verbose? |
When mainOnly = FALSE
, only the transcript location information will be returned,
Otherwise, a GRangesList
object containing gene regions
information will be added. Gene regions include: 2000 base pair upstream of the transcript
start site ($tss
)), 5'UTR ($fiveUTR
)), coding sequence ($cds
)),
exon ($exon
)), and 3'UTR ($threeUTR
)). The index
column is an internal
index that is used to facilitate data referral, which is meaningless for external use.
A single GRanges
(for main refgene data) object or a list incorporating
both GRanges
object (for main refgene data) and GRangesList
object
(for gene regions data).
ah <- AnnotationHub::AnnotationHub() refGene <- fetchRefSeqGene(ah, mainOnly = TRUE, verbose = TRUE) refGene