missingGenotypeRate {SeqVarTools} | R Documentation

## Missing genotype rate

### Description

Calculate missing genotype rate by variant or by sample

### Usage

    ## S4 method for signature 'SeqVarGDSClass'
    missingGenotypeRate(gdsobj, margin=c("by.variant", "by.sample"), use.names=FALSE)

### Arguments

`gdsobj` | A `SeqVarGDSClass` object with VCF data.
`margin` | Possible values are "by.variant" or "by.sample," indicating whether the calculation should be done over all samples for each variant, or over all variants for each sample.
`use.names` | A logical indicating whether to assign variant IDs as names of the output vector.

### Details

Calculates the fraction of missing genotypes in a GDS object, either by variant or by sample.

### Value

A numeric vector of missing genotype rates. If `margin="by.variant"`, the vector will have length equal to the number of variants in the GDS object. If `margin="by.sample"`, the vector will have length equal to the number of samples.

### Author(s)

Stephanie Gogarten

### See Also

`SeqVarGDSClass`, `applyMethod`, `getGenotype`

### Examples

    gds <- seqOpen(seqExampleFileName("gds"))
    head(missingGenotypeRate(gds, margin="by.variant"))
    head(missingGenotypeRate(gds, margin="by.sample"))
    seqClose(gds)

[Package SeqVarTools version 1.16.1 Index]