GRannot: Annotate genomic ranges data with gene region information.

In REMP: Repetitive Element Methylation Prediction

Description

GRannot is used to annotate a GRanges dataset with gene region information using refseq gene database

Usage

GRannot(object.GR, refgene, symbol = FALSE, verbose = FALSE)

Arguments

object.GR	An GRanges object of a genomic location database.
refgene	A complete refGene annotation database returned by fetchRefSeqGene (with parameter mainOnly = FALSE).
symbol	Logical parameter. Should the annotation return gene symbol?
verbose	Logical parameter. Should the function be verbose?

Details

The annotated gene region information includes: protein coding gene (InNM), noncoding RNA gene (InNR), 2000 base pair upstream of the transcript start site (InTSS), 5'UTR (In5UTR), coding sequence (InCDS), exon (InExon), and 3'UTR (In3UTR). The intergenic and intron regions can then be represented by the combination of these region data. The number shown in these columns represent the row number or 'index' column in the main refgene database obtained by fetchRefSeqGene.

Value

A GRanges or a GRangesList object containing refSeq Gene database.

Examples

data(Alu.hg19.demo)
if (!exists("refgene.hg19")) 
  refgene.hg19 <- fetchRefSeqGene(annotation.source = "AH", 
                                  genome = "hg19",
                                  verbose = TRUE)
Alu.hg19.demo.refGene <- GRannot(Alu.hg19.demo, refgene.hg19, verbose = TRUE)
Alu.hg19.demo.refGene

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