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

# Assignment of Haplotypes Based on SNP Dosages in Diploids and Polyploids

## Documentation for package ‘PolyHaplotyper’ version 1.0.1

- DESCRIPTION file
- User guides, package vignettes and other documentation

## Help Pages

allhap | Find all possible haplotypes
allHaplotypes | get all haplotypes for the given markers
build_ahccompletelist | generate a list with all haplotype combinations
calcMrkHaptable | produce a table of nr of markers vs nr of haplotypes
calcStatistics | calculate some statistics of the solutions of all haploblocks
checkmrkDosage | check a marker dosages matrix or data.frame
compareHapMrkDosages | compare haplotyping results with observed markers dosages
compareHapresults | compare two haplotyping results
demo_ped | pedigree
demo_snpdos | dosages of SNP alleles
expandHapdos | Add dropped rows back to haplotype dosage matrix
getFSfreqs | get all FS haplotype combinations expected from two parental haplotype combinations, with their frequencies
getGameteFreqs | get all gametes and their frequencies for a parental haplotype combination
hapcomb2hapdos | convert haplotype combinations to haplotype dosages
hapdos2hapcomb | convert haplotype dosages to haplotype combinations
hapdos2mrkdos | calculate the marker dosages resulting from haplotype dosage combinations
haploblock_df2list | convert a haploblock-defining data frame to a list
inferHaplotypes | infer haplotypes for one or more haploblocks
make.Happyinf.input | convert PolyHaplotyper input data to Happy-inf format
make.SATlotyper.input | convert PolyHaplotyper marker data to SATlotyper format
make.ShesisPlus.input | convert PolyHaplotyper marker data to ShesisPlus format
mergeReplicates | merge replicate samples in dosage matrix
mrkdid2mrkdos | get the marker dosages from mrkdids (marker dosage IDs)
mrkdos2mrkdid | get marker dosage IDs from marker dosages
overviewByFS | generate an overview of the results by haploblock and by FS family
padded | pad an integer (prefix with zeroes to a fixed length)
pedigreeHapCheck | check the consistency of haploblock genotypes over a pedigree
pedigreeSim2PH | convert the PedigreeSim true haplotypes to marker dosages and haplotype dosages
phblocks | List of markers per haploblock
phdos | dosages of SNP alleles
phFS | members of FS families
phpar | parents of FS families
phped | pedigree
phresults | haplotyping results
read.Happyinf.output | read the haplotyping results from the Happy-inf output
read.SATlotyper.output | read the haplotyping results from the SATlotyper output
read.ShesisPlus.output | Read the haplotyping results from the ShesisPlus output
run.SATlotyper | A simple interface to run SATlotyper
showOneFS | show marker and haplotype dosages for one FS family
totHapcombCount | calculate the total nr of possible haplotype combinations
usedhap | Find all used (inferred) haplotypes