extract.gt: Extract genotypes from SNP objects.

In stefanedwards/Siccuracy: Pipeline Package for AlphaImpute

Description

gt genotypes are stored with loci per row and samples per column. For the transposed, see extract.snps.

Usage

extract.gt(x, as.numeric, ...)

## S3 method for class 'vcfR'
extract.gt(x, as.numeric, ...)

## S3 method for class 'haps'
extract.gt(x, as.numeric = TRUE, ...)

## S3 method for class 'oxford'
extract.gt(x, as.numeric = TRUE, ..., as.integer = FALSE)

Arguments

x	Object to extract genotypes from.
as.numeric	Logical, when TRUE (default), return numeric matrix of SNP counts. When FALSE, character vector with both alleles separated by '/'.
...	Arguments passed on to vcfR's extract.gt.
as.integer	Rounds genotype dosages to whole integers.

Value

extract.gt returns a matrix with loci per row and samples per column.

See Also

extract.snps

stefanedwards/Siccuracy documentation built on May 30, 2019, 10:44 a.m.