humarray (version 1.2)

startSnp: Find closest SNPs to the starts of ranges

Description

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

Usage

startSnp(ranged = NULL, snp.info = NULL, chr = NULL, pos = NULL,
  start = T, end = F, nearest = T)

Arguments

ranged

A GRanges or RangedData object specifying the range(s) you wish to find SNPs near the starts 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 starts 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 starts of.

start

logical whether to return the SNP nearest the range starts

end

logical whether to return the SNP nearest the range ends

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 will be a vector which will have the same length as the input. Unless start=TRUE and end=TRUE, then will return a matrix which should have the same number of rows as the number of ranges entered. Note that endSnp() is equivalent to using this function when end=TRUE and start=FALSE, and rangeSnp() is the same as setting start=TRUE and end=TRUE.

Examples

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