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SNPRelate (version 1.6.4)

snpgdsApartSelection: 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.

See Also

snpgdsLDpruning

Examples

Run this code
# 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)

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