humarray (version 1.0.0)

get.t1d.subset: Obtain subset of ranged object overlapping known T1D associated genomic regions

Description

Return subset of a ranged object that overlaps ichip dense mapped regions. For type 1 diabetes and autoimmune disesase researchers.

Usage

get.t1d.subset(X, T1D.only = TRUE, build = NULL, ichip.regions = NULL, T1D.regions = NULL, invert = FALSE)

Arguments

X

GRanges or RangedData object, ranged object for which you want the T1D subset of ranges/SNPs.

T1D.only

logical, standard is to return type 1 diabetes (T1D) regions subset, but if this parameter is set to FALSE, will return the subset for all 12 autoimmune diseases mapped by the ImmunoChip consortium. (Cortes and Brown, 2010).

build

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

ichip.regions

GRanges or RangedData object, only use if you need to provide for a build other than 36 or 37 (hg18/hg19), or for multiple lookups to avoid reloading each time

T1D.regions

GRanges or RangedData object, only use if you need to provide for a build other than 36 or 37 (hg18/hg19), or for multiple lookups to avoid reloading each time.

invert

logical, set to TRUE if you wish to get the set of NON-T1D regions, or non-immune dense regions when T1D.only=FALSE.

Value

a GRanges object with the specified type 1 diabetes/autoimmune (or inverse) ranges

Examples

# all.reg <- rranges(10000)
# t1d <- get.t1d.subset(all.reg) # T1D regions
# non.autoimmune <- get.t1d.subset(T1D.only=FALSE,build=36,invert=TRUE) # non-autoimmune regions