Package: PolyPatEx 0.9.2

PolyPatEx: Paternity Exclusion in Autopolyploid Species

Functions to perform paternity exclusion via allele matching, in autopolyploid species having ploidy 4, 6, or 8. The marker data used can be genotype data (copy numbers known) or 'allelic phenotype data' (copy numbers not known).

Authors:Alexander Zwart

PolyPatEx_0.9.2.tar.gz
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PolyPatEx_0.9.2.tgz(r-4.4-any)PolyPatEx_0.9.2.tgz(r-4.3-any)
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PolyPatEx.pdf |PolyPatEx.html✨
PolyPatEx/json (API)

# Install 'PolyPatEx' in R:

install.packages('PolyPatEx', repos = c('https://aleczwart.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/aleczwart/polypatex/issues

Datasets:

FR_Genotype - Example genotype allele dataset
GF_Phenotype - Example phenotype allele dataset

On CRAN:

3.98 score 19 scripts 131 downloads 10 exports 1 dependencies

Last updated 9 years agofrom:328e042359. Checks:OK: 3 NOTE: 4. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Oct 16 2024
R-4.5-win	NOTE	Oct 16 2024
R-4.5-linux	NOTE	Oct 16 2024
R-4.4-win	NOTE	Oct 16 2024
R-4.4-mac	NOTE	Oct 16 2024
R-4.3-win	OK	Oct 16 2024
R-4.3-mac	OK	Oct 16 2024

Exports:convertToPhenot fixCSV foreignAlleles genotPPE inputData multilocusTypes phenotPPE potentialFatherCounts potentialFatherIDs preprocessData

Dependencies:gtools

Using PolyPatEx

Rendered fromPolyPatEx-vignette.Rnwusingutils::Sweaveon Oct 16 2024.

Last update: 2016-04-11
Started: 2016-01-14

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Polyploid paternity exclusion by allele matching.	PolyPatEx-package
Convert a genotype allele dataset to a phenotype dataset	convertToPhenot
Tidy a comma separated value (CSV) file	fixCSV
Identify foreign alleles	foreignAlleles
Example genotype allele dataset	FR_Genotype
Simple paternity exclusion for genotype allele data	genotPPE
Example phenotype allele dataset	GF_Phenotype
Read in, check and preprocess the allele dataset	inputData
Genotype summaries	multilocusTypes
Simple paternity exclusion for phenotype allele data	phenotPPE
Count potential fathers	potentialFatherCounts
Identify potential fathers	potentialFatherIDs
Check and preprocess an allele dataset	preprocessData