getGenotype {SeqVarTools} | R Documentation

## Get genotype data

### Description

Get matrix of genotype values from a GDS object

### Usage

    ## S4 method for signature 'SeqVarGDSClass'
    getGenotype(gdsobj, use.names=TRUE, parallel=FALSE)
    ## S4 method for signature 'SeqVarGDSClass'
    getGenotypeAlleles(gdsobj, use.names=TRUE, sort=FALSE, parallel=FALSE)
    ## S4 method for signature 'SeqVarGDSClass'
    refDosage(gdsobj, use.names=TRUE, ...)
    ## S4 method for signature 'SeqVarGDSClass'
    altDosage(gdsobj, use.names=TRUE, sparse=FALSE, parallel=FALSE, ...)
    ## S4 method for signature 'SeqVarGDSClass'
    expandedAltDosage(gdsobj, use.names=TRUE, sparse=FALSE, parallel=FALSE)
    ## S4 method for signature 'SeqVarGDSClass,numeric'
    alleleDosage(gdsobj, n=0, use.names=TRUE, parallel=FALSE)
    ## S4 method for signature 'SeqVarGDSClass,list'
    alleleDosage(gdsobj, n, use.names=TRUE, parallel=FALSE)

### Arguments

`gdsobj` | A `SeqVarGDSClass` object with VCF data.
`use.names` | A logical indicating whether to assign sample and variant IDs as dimnames of the resulting matrix.
`parallel` | Logical, numeric, or other value to control parallel processing; see `seqParallel` for details.
`sort` | Logical for whether to sort alleles lexographically ("G/T" instead of "T/G").
`sparse` | Logical for whether to return the alterate allele dosage as a sparse matrix using the linkMatrix package. In most cases, setting `sparse=TRUE` will dramatically reduce the size of the returned object.
`n` | An integer, vector, or list indicating which allele(s) to return dosage for. `n=0` is the reference allele, `n=1` is the first alternate allele, and so on.
`...` | Arguments to pass to `seqBlockApply`, e.g. `bsize` to set the block size.

### Details

In `getGenotype`, genotypes are coded as in the VCF file, where "0/0" is homozygous reference, "0/1" is heterozygous for the first alternate allele, "0/2" is heterozygous for the second alternate allele, etc. Separators are "/" for unphased and "|" for phased. If `sort=TRUE`, all returned genotypes will be unphased. Missing genotypes are coded as `NA`. Only haploid or diploid genotypes (the first two alleles at a given site) are returned.

If the argument `n` to`alleleDosage` is a single integer, the same allele is counted for all variants. If `n` is a vector with length=number of variants in the current filter, a different allele is counted for each variant. If `n` is a list, more than one allele can be counted for each variant. For example, if `n[[1]]=c(1,3)`, genotypes "0/1" and "0/3" will each have a dosage of 1 and genotype "1/3" will have a dosage of 2.

### Value

`getGenotype` and `getGenotypeAlleles` return a character matrix with dimensions [sample,variant] containing haploid or diploid genotypes.

`getGenotype` returns alleles as "0", "1", "2", etc. indicating reference and alternate alleles.

`getGenotypeAlleles` returns alleles as "A", "C", "G", "T". `sort=TRUE` sorts lexographically, which may be useful for comparing genotypes with data generated using a different reference sequence.

`refDosage` returns an integer matrix with the dosage of the reference allele: 2 for two copies of the reference allele ("0/0"), 1 for one copy of the reference allele, and 0 for two alternate alleles.

`altDosage` returns an integer matrix with the dosage of any alternate allele: 2 for two alternate alleles ("1/1", "1/2", etc.), 1 for one alternate allele, and 0 for no alternate allele (homozygous reference).

`expandedAltDosage` returns an integer matrix with the dosage of each alternate allele as a separate column. A variant with 2 possible alternate alleles will have 2 columns of output, etc.

`alleleDosage` with an integer argument returns an integer matrix with the dosage of the specified allele only: 2 for two copies of the allele ("0/0" if `n=0`, "1/1" if `n=1`, etc.), 1 for one copy of the specified allele, and 0 for no copies of the allele.

`alleleDosage` with a list argument returns a list of sample x allele matrices with the dosage of each specified allele for each variant.

### Author(s)

Stephanie Gogarten

### See Also

`SeqVarGDSClass`, `applyMethod`, `seqGetData`, `seqSetFilter`, `alleleFrequency`

### Examples

    gds <- seqOpen(seqExampleFileName("gds"))
    seqSetFilter(gds, variant.sel=1323:1327, sample.sel=1:10)
    nAlleles(gds)
    getGenotype(gds)
    getGenotypeAlleles(gds)
    refDosage(gds)
    altDosage(gds)
    expandedAltDosage(gds)
    alleleDosage(gds, n=0)
    alleleDosage(gds, n=1)
    alleleDosage(gds, n=c(0,1,0,1,0))
    alleleDosage(gds, n=list(0,c(0,1),0,c(0,1),1))
    seqClose(gds)

[Package SeqVarTools version 1.30.0 Index]