humarray (version 1.2)

get.genic.subset: Obtain subset of ranged object overlapping human genes

Description

Return subset of a ranged object that overlaps human genes (or custom ranges/exons). A wrapper for subsetByOverlaps that tries to ensure equivalent builds and chromosome labelling are taken care of automatically, and provides the default case of genic subsetting where no explicit ref parameter is required.

Usage

get.genic.subset(X, ref = NULL, build = NULL)

Arguments

X

GRanges or RangedData object, ranged object for which you want the genic subset of ranges/SNPs.

ref

GRanges or RangedData object, only use if you need to provide for a build other than 36 or 37 (hg18/hg19), or to use this function for another reference set, for instance you could provide an object with exons

build

e.g, 36/hg18 or 37/hg19, if left as NULL current getOption('ucsc') will be used.

Value

a GRanges object with the specified genic (or custom) ranges

See Also

get.gene.annot, get.exon.annot, subsetByOverlaps

Examples

# NOT RUN {
# all.reg <- rranges(1000) # random set of 1000 regions
# genic <- get.genic.subset(all.reg) # gene regions from the random set
# exonic <- get.genic.subset(all.reg,ref=get.exon.annot()) # exonic regions from the random set
# }