snpgdsApartSelection: Select SNPs with a basepair distance

In zhengxwen/SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

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

See Also

snpgdsLDpruning

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)

zhengxwen/SNPRelate documentation built on Nov. 19, 2024, 1:02 p.m.