R: Select SNPs with a basepair distance

snpgdsApartSelection {SNPRelate}

R Documentation

Select SNPs with a basepair distance

Description

Randomly selects SNPs for which each pair is at least as far apart as the specified basepair distance.

Usage

snpgdsApartSelection(chromosome, position, min.dist=100000,
    max.n.snp.perchr=-1, verbose=TRUE)

Arguments

`chromosome`	chromosome codes
`position`	SNP positions in base pair
`min.dist`	A numeric value to specify minimum distance required (in basepairs)
`max.n.snp.perchr`	A numeric value specifying the maximum number of SNPs to return per chromosome, "-1" means no number limit
`verbose`	if TRUE, show information

Value

A logical vector indicating which SNPs were selected.

Author(s)

Xiuwen Zheng

Examples

# open an example dataset (HapMap)
genofile <- snpgdsOpen(snpgdsExampleFileName())
genofile

chr <- read.gdsn(index.gdsn(genofile, "snp.chromosome"))
pos <- read.gdsn(index.gdsn(genofile, "snp.position"))

set.seed(1000)
flag <- snpgdsApartSelection(chr, pos, min.dist=250000, verbose=TRUE)
table(flag)

# close the genotype file
snpgdsClose(genofile)

[Package SNPRelate version 1.10.2 Index]