humarray (version 1.0.0)

get.exon.annot: Get exon names and locations from UCSC

Description

Various R packages assist in downloading exonic information but often the input required is complex, or several lines of code are required to initiate, returning an object that might require some manipulation to be useful. This function simplifies the job considerably, not necessarily requiring any arguments. The object returned can be a standard data.frame or a bioconductor GRanges/RangedData object. The raw annotation file downloaded will be kept in the working directory so that subsequent calls to this function run very quickly, and also allow use offline.

Usage

get.exon.annot(dir = NULL, build = NULL, bioC = T, transcripts = FALSE, GRanges = TRUE)

Arguments

dir

character, location to store file with the gene annotation. If NULL then getOption("save.annot.in.current")>=1 will result in this file being stored in the current directory, or if

build

string, currently 'hg18' or 'hg19' to specify which annotation version to use. Default is build-36/hg-18. Will also accept integers 36,37 as alternative arguments.

bioC

logical, whether to return the annotation as a ranged S4 object (GRanges or RangedData), or as a data.frame

transcripts

logical, if TRUE, return transcripts rather than exons

GRanges

logical, if TRUE and bioC is also TRUE, then returned object will be GRanges, otherwise it will be RangedData

Value

Returns a data.frame, GRanges or RangedData object, depending on input parameters. Contained will be HGNC gene labels, chromosome, start and end positions, transcript id number and name

Examples

setwd(tempdir())
get.exon.annot()