PolyPatEx: Paternity Exclusion in Autopolyploid Species
Version 0.9.2

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).

AuthorAlexander Zwart
Date of publication2016-04-11 09:06:29
MaintainerAlexander Zwart <Alec.Zwart@csiro.au>
LicenseGPL-3 + file LICENSE
Version0.9.2
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("PolyPatEx")

Getting started

Package overview
README.md

Popular man pages

fixCSV: Tidy a comma separated value (CSV) file
foreignAlleles: Identify foreign alleles
GF_Phenotype: Example phenotype allele dataset
PolyPatEx-package: Polyploid paternity exclusion by allele matching.
potentialFatherCounts: Count potential fathers
potentialFatherIDs: Identify potential fathers
preprocessData: Check and preprocess an allele dataset
See all...

All man pages Function index File listing

Man pages

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

Functions

FR_Genotype Man page
GF_Phenotype Man page
Phenot.getAllPossMPGenots Source code
Phenot.getProgenyStatusLookup Source code
PolyPatEx-package Man page
checkForValidPPEDataset Source code
checkForValidPPEOutputObj Source code
convertToPhenot Man page Source code
fixCSV Man page Source code
foreignAlleles Man page Source code
genotPPE Man page Source code
getAllPossGenotsFromPhenot Source code
getAllPossMPPhenotypes Source code
getMPPhenotypeFromCount Source code
getPossMPPhenotCounts Source code
getProgenyStatusGenot Source code
getProgenyStatusPhenot Source code
inputData Man page Source code
multilocusTypes Man page Source code
phenotPPE Man page Source code
potentialFatherCounts Man page Source code
potentialFatherIDs Man page Source code
preprocessData Man page Source code
removeMismatches Source code
stripNAs Source code

Files

inst
inst/tests
inst/tests/test-all.R
inst/extdata
inst/extdata/FR_Genotype.csv
inst/extdata/GF_Phenotype.csv
inst/doc
inst/doc/PolyPatEx-vignette.Rnw
inst/doc/PolyPatEx-vignette.pdf
NAMESPACE
data
data/FR_Genotype.rda
data/GF_Phenotype.rda
R
R/preprocessData.R
R/multilocusTypes.R
R/potentialFatherIDs.R
R/checkForValidPPEOutputObj.R
R/checkForValidPPEDataset.R
R/getMPPhenotypeFromCount.R
R/potentialFatherCounts.R
R/inputData.R
R/PolyPatEx-package.R
R/sysdata.rda
R/getProgenyStatusPhenot.R
R/CMPStatusLookupTablePloidy6.R
R/foreignAlleles.R
R/GF_Phenotype.R
R/getAllPossGenotsFromPhenot.R
R/removeMismatches.R
R/genotPPE.R
R/CMPStatusLookupTablePloidy4.R
R/Phenot.getAllPossMPGenots.R
R/getProgenyStatusGenot.R
R/stripNAs.R
R/FR_Genotype.R
R/fixCSV.R
R/phenotPPE.R
R/CMPStatusLookupTablePloidy8.R
R/getPossMPPhenotCounts.R
R/Phenot.getProgenyStatusLookup.R
R/getAllPossMPPhenotypes.R
R/convertToPhenot.R
vignettes
vignettes/PolyPatExDataSchematic.pdf
vignettes/PolyPatEx-vignette.Rnw
README.md
MD5
build
build/vignette.rds
DESCRIPTION
man
man/potentialFatherCounts.Rd
man/potentialFatherIDs.Rd
man/phenotPPE.Rd
man/fixCSV.Rd
man/preprocessData.Rd
man/genotPPE.Rd
man/multilocusTypes.Rd
man/inputData.Rd
man/foreignAlleles.Rd
man/FR_Genotype.Rd
man/convertToPhenot.Rd
man/PolyPatEx-package.Rd
man/GF_Phenotype.Rd
LICENSE
PolyPatEx documentation built on May 19, 2017, 1:55 p.m.

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