fetchRefSeqGene {REMP}R Documentation

Get RefSeq gene database

Description

fetchRefSeqGene is used to obtain refSeq gene database provided by AnnotationHub.

Usage

fetchRefSeqGene(ah, mainOnly = FALSE, verbose = FALSE)

Arguments

ah

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

mainOnly

Logical parameter. See details.

verbose

Logical parameter. Should the function be verbose?

Details

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.

Value

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).

Examples

ah <- AnnotationHub::AnnotationHub()
refGene <- fetchRefSeqGene(ah, mainOnly = TRUE, verbose = TRUE)
refGene


[Package REMP version 1.4.1 Index]