missingGenotypeRate: Missing genotype rate
In SeqVarTools: Tools for variant data

Description Usage Arguments Details Value Author(s) See Also Examples

Calculate missing genotype rate by variant or by sample

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

`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.
`parallel`	Logical, numeric, or other value to control parallel processing; see `seqParallel` for details.

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

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.

Stephanie Gogarten

SeqVarGDSClass, applyMethod, getGenotype

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