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allelematch (version 2.5.1)

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

Description

Tools for the identification of unique of multilocus genotypes when both genotyping error and missing data may be present. The package is targeted at those working with large datasets and databases containing multiple samples of each individual, a situation that is common in conservation genetics, and particularly in non-invasive wildlife sampling applications. Functions explicitly incorporate missing data, and can tolerate allele mismatches created by genotyping error. If you use this tool, please cite the package using the journal article in Molecular Ecology Resources (Galpern et al., 2012). Please use citation('allelematch') to call the full citation. For users with access to the associated journal article, tutorial material is also available as supplementary material to the article describing this software, the citation for which can be called using citation('allelematch').

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Version

Install

install.packages('allelematch')

Monthly Downloads

336

Version

2.5.1

License

GPL-3

Maintainer

Todd Cross

Last Published

April 15th, 2019

Functions in allelematch (2.5.1)

amDataset

Prepare a dataset for use with allelematch
allelematch-package

Identifying Unique Multilocus Genotypes where Genotyping Error and Missing Data may be Present
amAlleleFreq

Determine allele frequencies
amUniqueProfile

Determine optimal parameter values for the identification of unique genotypes
amUnique

Identification of unique genotypes
amMatrix

Produce a dissimilarity matrix for pairs of multilocus genotypes
amPairwise

Pairwise matching of multilocus genotypes
amCSSForHTML

Produce cascading style sheet (CSS) for HTML
amCluster

Clustering of multilocus genotypes
amExampleData

Data sets to support the tutorials in the supplementary documentation and examples in the manual.