Man pages for PolyHaplotyper
Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

allhapFind all possible haplotypes
allHaplotypesget all haplotypes for the given markers
build_ahccompletelistgenerate a list with all haplotype combinations
calcMrkHaptableproduce a table of nr of markers vs nr of haplotypes
calcStatisticscalculate some statistics of the solutions of all haploblocks
checkmrkDosagecheck a marker dosages matrix or data.frame
compareHapMrkDosagescompare haplotyping results with observed markers dosages
compareHapresultscompare two haplotyping results
demo_snpdosdosages of SNP alleles
expandHapdosAdd dropped rows back to haplotype dosage matrix
getFSfreqsget all FS haplotype combinations expected from two parental...
getGameteFreqsget all gametes and their frequencies for a parental...
hapcomb2hapdosconvert haplotype combinations to haplotype dosages
hapdos2hapcombconvert haplotype dosages to haplotype combinations
hapdos2mrkdoscalculate the marker dosages resulting from haplotype dosage...
haploblock_df2listconvert a haploblock-defining data frame to a list
inferHaplotypesinfer haplotypes for one or more haploblocks
make.Happyinf.inputconvert PolyHaplotyper input data to Happy-inf format
make.SATlotyper.inputconvert PolyHaplotyper marker data to SATlotyper format
make.ShesisPlus.inputconvert PolyHaplotyper marker data to ShesisPlus format
mergeReplicatesmerge replicate samples in dosage matrix
mrkdid2mrkdosget the marker dosages from mrkdids (marker dosage IDs)
mrkdos2mrkdidget marker dosage IDs from marker dosages
overviewByFSgenerate an overview of the results by haploblock and by FS...
paddedpad an integer (prefix with zeroes to a fixed length)
pedigreeHapCheckcheck the consistency of haploblock genotypes over a pedigree
pedigreeSim2PHconvert the PedigreeSim true haplotypes to marker dosages and...
phblocksList of markers per haploblock
phdosdosages of SNP alleles
phFSmembers of FS families
phparparents of FS families
phresultshaplotyping results
read.Happyinf.outputread the haplotyping results from the Happy-inf output
read.SATlotyper.outputread the haplotyping results from the SATlotyper output
read.ShesisPlus.outputRead the haplotyping results from the ShesisPlus output
run.SATlotyperA simple interface to run SATlotyper
showOneFSshow marker and haplotype dosages for one FS family
totHapcombCountcalculate the total nr of possible haplotype combinations
usedhapFind all used (inferred) haplotypes
PolyHaplotyper documentation built on June 17, 2021, 5:12 p.m.