alleleFrequency: Allele frequency

In smgogarten/SeqVarTools: Tools for variant data

Allele frequency

Description

Calculate allele frequency for each variant

Usage

## S4 method for signature 'SeqVarGDSClass'
alleleFrequency(gdsobj, n=0, use.names=FALSE, parallel=FALSE)
## S4 method for signature 'SeqVarData'
alleleFrequency(gdsobj, n=0, use.names=FALSE, sex.adjust=TRUE, male.diploid=TRUE,
    genome.build=c("hg19", "hg38"), parallel=FALSE)
## S4 method for signature 'SeqVarGDSClass'
alleleCount(gdsobj, n=0, use.names=FALSE, parallel=FALSE)
## S4 method for signature 'SeqVarData'
alleleCount(gdsobj, n=0, use.names=FALSE, sex.adjust=TRUE, male.diploid=TRUE,
    genome.build=c("hg19", "hg38"), parallel=FALSE)
## S4 method for signature 'SeqVarData'
minorAlleleCount(gdsobj, use.names=FALSE, sex.adjust=TRUE, male.diploid=TRUE,
    genome.build=c("hg19", "hg38"), parallel=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.
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.
male.diploid	Logical for whether males on sex chromosomes are coded as diploid.
genome.build	A character sting indicating genome build; used to identify pseudoautosomal regions on the X and Y chromosomes.
parallel	Logical, numeric, or other value to control parallel processing; see seqParallel for details.

Details

Frequency or count 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 and count 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. If the ploidy of the "genotype" node in the GDS file is 2, the default assumption is that genotypes for males on sex chromosomes are coded as diploid, "0/0" or "1/1". If this is not the case, use male.diploid=FALSE.

For multiallelic variants, the minor allele count will be the smaller of the reference allele count or the sum of all alternate allele counts.

Value

A numeric vector of allele frequencies.

Author(s)

Stephanie Gogarten

See Also

chromWithPAR, SeqVarGDSClass, applyMethod, heterozygosity

Examples

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

smgogarten/SeqVarTools documentation built on July 4, 2023, 2:34 a.m.