humarray (version 1.2)

endSnp: Find closest SNPs to the ends of ranges

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

# NOT RUN {
endSnp(chr=c(1:3),pos=cbind(c(100000,200000,300000),c(30000000,4000000,10000000)))
endSnp(rranges())
# }