SNP selection

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Description

Create a list of candidate SNPs based on specified criteria

Usage

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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

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# 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)

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