gl2hiphop: Converts a genlight objects into hiphop format

In green-striped-gecko/dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Converts a genlight objects into hiphop format

Description

This function exports genlight objects to the format used by the parentage assignment R package hiphop. Hiphop can be used for paternity and maternity assignment and outperforms conventional methods where closely related individuals occur in the pool of possible parents. The method compares the genotypes of offspring with any combination of potentials parents and scores the number of mismatches of these individuals at bi-allelic genetic markers (e.g. Single Nucleotide Polymorphisms).

Usage

gl2hiphop(x, verbose = NULL)

Arguments

x	Name of the genlight object containing the SNP data [required].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity].

Value

Dataframe containing all the genotyped individuals (offspring and potential parents) and their genotypes scored using bi-allelic markers.

Author(s)

Luis Mijangos (Post to https://groups.google.com/d/forum/dartr)

References

Cockburn, A., Penalba, J.V.,Jaccoud, D.,Kilian, A., Brouwer, L.,Double, M.C., Margraf, N., Osmond, H.L., van de Pol, M. and Kruuk, L.E.B.(in revision). HIPHOP: improved paternity assignment among close relatives using a simple exclusion method for bi-allelic markers. Molecular Ecology Resources, DOI to be added upon acceptance

Examples

result <- gl2hiphop(testset.gl)

green-striped-gecko/dartR documentation built on Sept. 7, 2024, 4:15 a.m.