snpgdsSelectSNP {SNPRelate} | R Documentation

## 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)

[Package SNPRelate version 1.18.1 Index]