allHaplotypes           get all haplotypes for the given markers
allhap                  Find all possible haplotypes
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
phFS                    members of FS families
phblocks                List of markers per haploblock
phdos                   dosages of SNP alleles
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
