snpgdsSelectSNP: SNP selection

In SNPRelate: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)

Description

Create a list of candidate SNPs based on specified criteria

Usage

snpgdsSelectSNP(gdsobj, sample.id=NULL, snp.id=NULL, autosome.only=TRUE,
	remove.monosnp=TRUE, maf=NaN, missing.rate=NaN, verbose=TRUE)

Arguments

gdsobj	a GDS file object (gds.class)
sample.id	a vector of sample id specifying selected samples; if NULL, all samples are used
snp.id	a vector of snp id specifying selected SNPs; if NULL, all SNPs are used
autosome.only	if TRUE, use autosomal SNPs only
remove.monosnp	if TRUE, remove monomorphic SNPs
maf	to use the SNPs with ">= maf" only; if NaN, no any MAF threshold
missing.rate	to use the SNPs with "<= missing.rate" only; if NaN, no any missing threshold
verbose	if TRUE, show information

Value

Return a list of snp ids.

Author(s)

Xiuwen Zheng

See Also

snpgdsSampMissrate, snpgdsSNPRateFreq, snpgdsLDpruning

Examples

# open an example dataset (HapMap)
genofile <- openfn.gds(snpgdsExampleFileName())

snpset <- snpgdsSelectSNP(genofile, maf=0.05, missing.rate=0.95)

# close the genotype file
closefn.gds(genofile)

SNPRelate documentation built on May 2, 2019, 4:56 p.m.