allelematch: Identifying unique multilocus genotypes where genotyping error and missing data may be present
Version 2.5

This package provides 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 find this. Due to changing CRAN policy, and the size and compile time of the vignettes, they can no longer be distributed with this package. Please contact the package primary author, or visit the allelematch site for a complete vignette (http://nricaribou.cc.umanitoba.ca/allelematch/). For users with access to academic literature, tutorial material is also available as supplementary material to the article describing this software.

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AuthorPaul Galpern <pgalpern@gmail.com>
Date of publication2014-09-19 00:14:49
MaintainerPaul Galpern <pgalpern@gmail.com>
LicenseGPL (>= 2)
Version2.5
URL http://nricaribou.cc.umanitoba.ca/allelematch/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("allelematch")

Man pages

allelematch-package: Identification of unique multilocus genotypes
amAlleleFreq: Determine allele frequencies
amCluster: Clustering of multilocus genotypes
amCSSForHTML: Produce cascading style sheet (CSS) for HTML
amDataset: Prepare a dataset for use with allelematch
amExampleData: Data sets to support the tutorials in the supplementary...
amMatrix: Produce a dissimilarity matrix for pairs of multilocus...
amPairwise: Pairwise matching of multilocus genotypes
amUnique: Identification of unique genotypes
amUniqueProfile: Determine optimal parameter values for the identification of...

Functions

allelematch Man page
allelematch-package Man page
allelematch-tutorial Man page
amAlleleFreq Man page Source code
amCSSForHTML Man page Source code
amCSV.amCluster Man page Source code
amCSV.amPairwise Man page Source code
amCSV.amUnique Man page Source code
amCluster Man page Source code
amDataset Man page Source code
amExample1 Man page
amExample2 Man page
amExample3 Man page
amExample4 Man page
amExample5 Man page
amExampleData Man page
amHTML.amCluster Man page Source code
amHTML.amPairwise Man page Source code
amHTML.amUnique Man page Source code
amMatrix Man page Source code
amPairwise Man page Source code
amUnique Man page Source code
amUniqueProfile Man page Source code
print.amAlleleFreq Man page Source code
print.amDataset Man page Source code
summary.amCluster Man page Source code
summary.amPairwise Man page Source code
summary.amUnique Man page Source code

Files

inst
inst/CITATION
NAMESPACE
data
data/amExample4.RData
data/amExample1.RData
data/amExample5.RData
data/amExample3.RData
data/amExample2.RData
R
R/allelematch.r
MD5
DESCRIPTION
man
man/amExampleData.Rd
man/amCluster.Rd
man/amUniqueProfile.Rd
man/amPairwise.Rd
man/amMatrix.Rd
man/amAlleleFreq.Rd
man/amDataset.Rd
man/allelematch-package.Rd
man/amUnique.Rd
man/amCSSForHTML.Rd
allelematch documentation built on May 19, 2017, 7:22 p.m.