Description Usage Arguments Value Examples
This function will always use the build in getOption('ucsc'), so use options() if it needs to change.
1 |
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. |
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.
1 2 3 | 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
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