Assignment of Haplotypes Based on SNP Dosages in Diploids and
Polyploids
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Documentation for package ‘PolyHaplotyper’ version 1.0.1
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 |