humarray (version 1.2)

snps.in.range: Retrieve SNP ids or positions in specified range

Description

This function will always use the build in getOption('ucsc'), so use options() if it needs to change.

Usage

snps.in.range(chr, start = NA, end = start, ids = TRUE)

Arguments

chr

integer, chromosome, should be a number from 1 to 25, where 23,24,25 are X,Y,MT Alternatively chr can be a RangedData or GRanges object in which case SNP lists will be returned in a list for each row of the ranges object.

start

integer, genomic position to define the start of the range to look for SNPs, should be between 1 and the length of the chromosome 'chr'

end

integer, genomic position to define the end of the range to look for SNPs, should be between 1 and the length of the chromosome 'chr', and >= start

ids

logical, if TRUE will return snp ids (chip ids, for rs-ids, use id.to.rs on the output), or if FALSE will return the chromosome positions of the SNPs.

Value

Set of SNP ids (when ids=TRUE), or otherwise genomic positions within chromosome 'chr', that fall within the genomic range described by the chr, start, and end parameters. Alternatively, if chr is a RangedData or GRanges object then multiple SNP lists will be returned in a list for each row of the ranges object.

Examples

# NOT RUN {
snps.in.range(1,9000000,10000000)
snps.in.range(10,19000000,20000000,ids=TRUE)
snps.in.range(10,19000000,20000000,ids=FALSE) # return positions instead of rs-ids
# }