endSnp: Find closest SNPs to the ends of ranges

In humarray: Simplify Analysis and Annotation of Human Microarray Datasets

Description

For given genome ranges (GRanges/RangedData) will try to find the closest snps to the end of the ranges.

Usage

endSnp(ranged = NULL, snp.info = NULL, chr = NULL, pos = NULL,
  nearest = T)

Arguments

ranged	A GRanges or RangedData object specifying the range(s) you wish to find SNPs near the ends of. Alternatively leave this parameter as NULL and specify ranges using chr, pos
snp.info	ChipInfo/GRanges/Ranged data object describing the SNPs relevant to your query, e.g, SNPs on the chip you are using. If left NULL, the SNP set used will be that retrieved by chip.support() which will depend on your options() settings, see ?chip.support for more info
chr	optional alternative to 'ranged' input, use in conjunction with 'pos' to specify the ranges to find the SNPs near the ends of.
pos	matrix with 2 columns for start, end positions, or a single column if all ranges are SNPs. An optional alternative to 'ranged' input, use in conjunction with 'chr' to specify the ranges to find the SNPs near the ends of.
nearest	will preferably find an exact match but if nearest=TRUE, will fall-back on nearest match, even if slightly outside the range.

Value

a list of SNP-ids (rownames of 'snp.info') fulfilling the criteria, the output vector (character) should be the same length as the number of ranges entered.

Examples

endSnp(chr=c(1:3),pos=cbind(c(100000,200000,300000),c(30000000,4000000,10000000)))
endSnp(rranges())

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