SNP selection

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

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

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# 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)

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