extract.gt: Extract genotypes from SNP objects.

Description Usage Arguments Value See Also

View source: R/extract_.R

Description

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

Usage

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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 Dec. 14, 2017, 7:41 p.m.