humarray (version 1.0.0)

get.immunog.locs: Retrieve locations of Immunoglobin regions across the genome

Description

Returns the locations of immunoglobin regions in the human genome, for a given build, as a list by chromosome, text vector, or GRanges/RangedData object. For instance, for CNV research, these regions are known to be highly structurally complex and can lead to false positive CNV-calls, so are often excluded.

Usage

get.immunog.locs(build = NULL, bioC = TRUE, text = FALSE, GRanges = TRUE)

Arguments

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

text

logical, whether to return locations as a text vector of the form: chrN:xxxx-xxxx

GRanges

logical, whether to return a GRanges object, or FALSE to return RangedData

Value

Returns a list, GRanges or RangedData object, depending on input parameters. Contained will be immunoglobin chromosome, start and end positions.

Examples

get.immunog.locs()
get.immunog.locs(bioC=FALSE)
get.immunog.locs(text=TRUE,build=37)