expand.nsnp: Expand genomic locations to the ranges covering the 'n'...

In humarray: Simplify Analysis and Annotation of Human Microarray Datasets

Description

Sometimes for chip data we want to create windows around some locus, and fixed distance [see flank()], recombination distance [see recomWindow()] or a number of SNPs might be used. This function allows expansion of regions according to a set number of SNPs. The result gives two regions for each row of a GRanges or RangedData object describing the start and end of the left flanking 'nsnp' region, and right flanking 'nsnp' region respectively.

Usage

expand.nsnp(ranged, snp.info = NULL, nsnp = 10, add.chr = FALSE)

Arguments

ranged	a GRanges or RangedData object describing the locations for which we want to find regions encompassing 'nsnps' closest SNPs.
snp.info	An object of type: ChipInfo, RangedData or GRanges, describing the set of SNPs you are using (e.g, chip annotation). If left as null the ChipInfo object from chip.support() with default options() will be used
nsnp	Number of nearest SNPs to return for each location
add.chr	logical, whether to add a chromosome column for the output object

Value

Two regions for each row of a the 'ranged' object describing the start and end of the left flanking 'nsnp' region, and right flanking 'nsnp' region respectively. If 'ranged' has rownames these should stay in the same order in the resulting object. Chromosome will be the final column if you set add.chr=TRUE.

See Also

nearest.snp, chip.support, recomWindow

Examples

rngs <- rranges()
# not run - slow ~5 seconds # expand.nsnp(rngs)
# not run - slow ~5 seconds # expand.nsnp(rngs,add.chr=TRUE)

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