snpgdsSelectSNP: SNP selection

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

SNP selection

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	an object of class SNPGDSFileClass, a SNP GDS file
sample.id	a vector of sample id specifying selected samples; if NULL, all samples will be used
snp.id	a vector of snp id specifying selected SNPs; if NULL, all SNPs will be used
autosome.only	if TRUE, use autosomal SNPs only; if it is a numeric or character value, keep SNPs according to the specified chromosome
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 <- snpgdsOpen(snpgdsExampleFileName())

snpset <- snpgdsSelectSNP(genofile, maf=0.05, missing.rate=0.95)
length(snpset)
# 7502

# close the genotype file
snpgdsClose(genofile)

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