snpgdsSNPRateFreq {SNPRelate} | R Documentation

## Allele Frequency, Minor Allele Frequency, Missing Rate of SNPs

### Description

Calculate the allele frequency, minor allele frequency and missing rate per SNP.

### Usage

    snpgdsSNPRateFreq(gdsobj, sample.id=NULL, snp.id=NULL, with.id=FALSE,
        with.sample.id=FALSE, with.snp.id=FALSE)

### 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
`with.id` | if `TRUE`, return both sample and SNP IDs
`with.sample.id` | if `TRUE`, return sample IDs
`with.snp.id` | if `TRUE`, return SNP IDs

### Value

Return a list:

`AlleleFreq` | allele frequencies
`MinorFreq` | minor allele frequencies
`MissingRate` | missing rates
`sample.id` | sample id, if `with.id=TRUE` or `with.sample.id=TRUE`
`snp.id` | SNP id, if `with.id=TRUE` or `with.snp.id=TRUE`

### Author(s)

Xiuwen Zheng

### See Also

`snpgdsSampMissRate`

### Examples

    # open an example dataset (HapMap)
    genofile <- snpgdsOpen(snpgdsExampleFileName())

    RV <- snpgdsSNPRateFreq(genofile, with.snp.id=TRUE)
    head(data.frame(RV))

    hist(RV$AlleleFreq, breaks=128)
    summary(RV$MissingRate)

    # close the file
    snpgdsClose(genofile)

[Package SNPRelate version 1.18.1 Index]