get.t1d.subset: Obtain subset of ranged object overlapping known T1D...
In humarray: Simplify Analysis and Annotation of Human Microarray Datasets

Description Usage Arguments Value Examples

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

1 2	get.t1d.subset(X, T1D.only = TRUE, build = NULL, ichip.regions = NULL, T1D.regions = NULL, invert = FALSE)

`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.

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

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# 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

humarray documentation built on Nov. 20, 2017, 1:05 a.m.