R: Allele frequency

alleleFrequency {SeqVarTools}

R Documentation

Allele frequency

Description

Calculate allele frequency for each variant

Usage

## S4 method for signature 'SeqVarGDSClass'
alleleFrequency(gdsobj, n=0, use.names=FALSE)
## S4 method for signature 'SeqVarData'
alleleFrequency(gdsobj, n=0, use.names=FALSE, sex.adjust=TRUE, genome.build=c("hg19", "hg38"))

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.
`sex.adjust`	Logical for whether to adjust frequency calculations based on sex. If `TRUE`, X chromosome frequency (excluding the PAR) will be calculated assuming the dosage of the specifed allele for males is half that for females. Y chromosome frequency will be calculated using males only.
`genome.build`	A character sting indicating genome build.

Details

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

The SeqVarData method will calculate frequency correctly for X and Y chromosomes, provided a column "sex" is included in the sampleData slot with values "M"/"F" or 1/2. Arguments given to this method are passed to the parent method for SeqVarGDSClass.

Value

A numeric vector of allele frequencies.

Author(s)

Stephanie Gogarten

Examples

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

[Package SeqVarTools version 1.16.1 Index]