SeqVarTools (version 1.10.0)

alleleFrequency: Allele frequency

Description

Calculate allele frequency for each variant

Usage

"alleleFrequency"(gdsobj, n=0, use.names=FALSE)

Arguments

gdsobj

A SeqVarGDSClass object with VCF data.

n

An integer indicating which allele to calculate the frequency of. n=0 is the reference allele, n=1 is the first alternate allele, and so on.

use.names

A logical indicating whether to assign variant IDs as names of the output vector.

Value

A numeric vector of allele frequencies.

Details

Frequency can be calculated over any allele, specified by the argument n. Default is the reference allele frequency (n=0).

See Also

SeqVarGDSClass, applyMethod, heterozygosity

Examples

gds <- seqOpen(seqExampleFileName("gds"))
head(alleleFrequency(gds))
head(alleleFrequency(gds, n=1))
head(alleleFrequency(gds, n=2))
seqClose(gds)