| allelematch-package {allelematch} | R Documentation |
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
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 (pgalpern@gmail.com)
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