apartSnpSelection {GWASTools} | R Documentation |
Randomly selects SNPs for which each pair is at least as far apart as the specified basepair distance.
apartSnpSelection(chromosome, position, min.dist = 1e+05, init.sel = NULL, max.n.chromosomes = -1, verbose = TRUE)
chromosome |
An integer vector containing the chromosome for each SNP. Valid values are 1-26, any other value will be interpreted as missing and not selected. |
position |
A numeric vector of the positions (in basepairs) of the SNPs. |
min.dist |
A numeric value to specify minimum distance required (in basepairs). |
init.sel |
A logical vector indicating the initial SNPs to be included. |
max.n.chromosomes |
A numeric value specifying the maximum number of SNPs to return per chromosome, "-1" means no number limit. |
verbose |
A logical value specifying whether to show progress information while running. |
apartSnpSelection
selects SNPs randomly with the condition that
they are at least as far apart as min.dist
in basepairs. The
starting set of SNPs can be specified with init.sel
.
A logical vector indicating which SNPs were selected.
Xiuwen Zheng
library(GWASdata) data(affy_snp_annot) pool <- affy_snp_annot$chromosome < 23 rsnp <- apartSnpSelection(affy_snp_annot$chromosome, affy_snp_annot$position, min.dist=15000, init.sel=pool)