extract.snps: #' Extracts #' #' @inheritParams extract.snps #' @return...

Description Usage Arguments Value

Description

The SNP format lists samples as rows and loci as columns. it is simply gt transposed. The SNP format is always numeric.

Usage

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extract.snps(x, as.integer)

## S3 method for class 'haps'
extract.snps(x, as.integer = FALSE)

## S3 method for class 'vcfR'
extract.snps(x, as.integer = FALSE, ...)

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

Arguments

x

Object to extract genotypes from.

as.integer

Rounds genotype dosages to whole integers.

...

Arguments passed on to vcfR's extract.gt.

Value

extract.snps returns matrix with indivduals by row, with numeric genotypes.


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