PolyPatEx: Paternity Exclusion in Autopolyploid Species

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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).

Author
Alexander Zwart
Date of publication
2016-04-11 09:06:29
Maintainer
Alexander Zwart <Alec.Zwart@csiro.au>
License
GPL-3 + file LICENSE
Version
0.9.2

View on CRAN

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

Files in this package

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