as.segsites.GENOME {coala}

Convert PopGenome Data into Coala's Format

Description

Using this function, you can convert genetic data imported with the package PopGenome into coala's segsites format. See as.segsites for general information on converting genetic data for coala.

Usage

## S3 method for class 'GENOME'
as.segsites(data, only_synonymous = FALSE, ...)

Arguments

data

The GENOME data from PopGenome.

only_synonymous

Only import synonymous SNPs if set to TRUE. This requires that PopGenome knows where coding regions are., e.g. by using gff files.

...

Ignored.

Details

This function imports all loci from the GENOME object that have at least one valid site ([e-mail]). The number of valid sites is used as length of a locus.

See Also

An example and additional instructions are provided in the coala-data-import vignette