Package: PolyHaplotyper 1.0.1

Roeland E. Voorrips

PolyHaplotyper: Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

Infer the genetic composition of individuals in terms of haplotype dosages for a haploblock, based on bi-allelic marker dosages, for any ploidy level. Reference: Voorrips and Tumino: PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data. Submitted to BMC Bioinformatics (2021).

Authors:Roeland E. Voorrips

PolyHaplotyper_1.0.1.tar.gz
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PolyHaplotyper.pdf |PolyHaplotyper.html✨
PolyHaplotyper/json (API)

# Install 'PolyHaplotyper' in R:
install.packages('PolyHaplotyper', repos = c('https://polyploids.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 3 scripts 143 downloads 33 exports 1 dependencies

Last updated 4 years agofrom:c733cbb692. Checks:OK: 7. Indexed: no.

TargetResultDate
Doc / VignettesOKDec 15 2024
R-4.5-winOKDec 15 2024
R-4.5-linuxOKDec 15 2024
R-4.4-winOKDec 15 2024
R-4.4-macOKDec 15 2024
R-4.3-winOKDec 15 2024
R-4.3-macOKDec 15 2024

Exports:allhapallHaplotypesbuild_ahccompletelistcalcMrkHaptablecalcStatisticscheckmrkDosagecompareHapMrkDosagescompareHapresultsexpandHapdosgetFSfreqsgetGameteFreqshapcomb2hapdoshapdos2hapcombhapdos2mrkdoshaploblock_df2listinferHaplotypesmake.Happyinf.inputmake.SATlotyper.inputmake.ShesisPlus.inputmergeReplicatesmrkdid2mrkdosmrkdos2mrkdidoverviewByFSpaddedpedigreeHapCheckpedigreeSim2PHread.Happyinf.outputread.SATlotyper.outputread.ShesisPlus.outputrun.SATlotypershowOneFStotHapcombCountusedhap

Dependencies:XML

PolyHaplotyper vignette

Roeland E. Voorrips

Rendered fromPolyHaplotyper.Rmdusingknitr::rmarkdownon Dec 15 2024.

Last update: 2021-02-10
Started: 2021-02-10

Readme and manuals

Help Manual

Help pageTopics
Find all possible haplotypesallhap
get all haplotypes for the given markersallHaplotypes
generate a list with all haplotype combinationsbuild_ahccompletelist
produce a table of nr of markers vs nr of haplotypescalcMrkHaptable
calculate some statistics of the solutions of all haploblockscalcStatistics
check a marker dosages matrix or data.framecheckmrkDosage
compare haplotyping results with observed markers dosagescompareHapMrkDosages
compare two haplotyping resultscompareHapresults
pedigreedemo_ped
dosages of SNP allelesdemo_snpdos
Add dropped rows back to haplotype dosage matrixexpandHapdos
get all FS haplotype combinations expected from two parental haplotype combinations, with their frequenciesgetFSfreqs
get all gametes and their frequencies for a parental haplotype combinationgetGameteFreqs
convert haplotype combinations to haplotype dosageshapcomb2hapdos
convert haplotype dosages to haplotype combinationshapdos2hapcomb
calculate the marker dosages resulting from haplotype dosage combinationshapdos2mrkdos
convert a haploblock-defining data frame to a listhaploblock_df2list
infer haplotypes for one or more haploblocksinferHaplotypes
convert PolyHaplotyper input data to Happy-inf formatmake.Happyinf.input
convert PolyHaplotyper marker data to SATlotyper formatmake.SATlotyper.input
convert PolyHaplotyper marker data to ShesisPlus formatmake.ShesisPlus.input
merge replicate samples in dosage matrixmergeReplicates
get the marker dosages from mrkdids (marker dosage IDs)mrkdid2mrkdos
get marker dosage IDs from marker dosagesmrkdos2mrkdid
generate an overview of the results by haploblock and by FS familyoverviewByFS
pad an integer (prefix with zeroes to a fixed length)padded
check the consistency of haploblock genotypes over a pedigreepedigreeHapCheck
convert the PedigreeSim true haplotypes to marker dosages and haplotype dosagespedigreeSim2PH
List of markers per haploblockphblocks
dosages of SNP allelesphdos
members of FS familiesphFS
parents of FS familiesphpar
pedigreephped
haplotyping resultsphresults
read the haplotyping results from the Happy-inf outputread.Happyinf.output
read the haplotyping results from the SATlotyper outputread.SATlotyper.output
Read the haplotyping results from the ShesisPlus outputread.ShesisPlus.output
A simple interface to run SATlotyperrun.SATlotyper
show marker and haplotype dosages for one FS familyshowOneFS
calculate the total nr of possible haplotype combinationstotHapcombCount
Find all used (inferred) haplotypesusedhap