allelematch-package: Identification of unique multilocus genotypes

In allelematch: Identifying Unique Multilocus Genotypes where Genotyping Error and Missing Data may be Present

Identification of unique multilocus genotypes

Description

Tools for the identification of unique of multilocus genotypes when both genotyping error and missing data may be present; targeted for use with large datasets and databases containing multiple samples of each individual (a common situation in conservation genetics, particularly in non-invasive wildlife sampling applications). Functions explicitly incorporate missing data and can tolerate allele mismatches created by genotyping error.

Details

Package:	allelematch
Type:	Package
Version:	2.5.2
Date:	2023-05-18
License:	GPL (>= 2)
Requires:	dynamicTreeCut
LazyLoad:	yes

Supplementary documentation describing the operation of the software in detail and illustrating the use of the software using tutorials is available as a vignette. It is installed with the package and linked from the package index help page. An online version is also available via the Data S1 Supplementary documentation and tutorials (PDF) located at \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1111/j.1755-0998.2012.03137.x")}.

Simulations examining the performance of these tools have also been performed, and results are available in the publication associated with this package. Please refer to the publication:

Galpern P, Manseau, M, Hettinga P, Smith K, and Wilson P. (2012) allelematch: an R package for identifying unique multilocus genotypes where genotype error and missing data may be present. Molecular Ecology Resources 12:771-778.

Use citation("allelematch") for the full citation. Please also use this publication when citing the package.

An important core element of the package is dynamic tree cutting, and this is made possible via the cutreeHybrid function within the dynamicTreeCut package for R (Langfelder et al., 2008).

Author(s)

Paul Galpern ([e-mail])

References

Langfelder P, Zhang B, Horvath S. (2008) Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics, 24, 719

allelematch documentation built on May 29, 2024, 7:45 a.m.