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"demo_ped" ] }, { "page": "demo_snpdos", "title": "dosages of SNP alleles", "topics": [ "demo_snpdos" ] }, { "page": "expandHapdos", "title": "Add dropped rows back to haplotype dosage matrix", "topics": [ "expandHapdos" ] }, { "page": "getFSfreqs", "title": "get all FS haplotype combinations expected from two parental haplotype combinations, with their frequencies", "topics": [ "getFSfreqs" ] }, { "page": "getGameteFreqs", "title": "get all gametes and their frequencies for a parental haplotype combination", "topics": [ "getGameteFreqs" ] }, { "page": "hapcomb2hapdos", "title": "convert haplotype combinations to haplotype dosages", "topics": [ "hapcomb2hapdos" ] }, { "page": "hapdos2hapcomb", "title": "convert haplotype dosages to haplotype combinations", "topics": [ "hapdos2hapcomb" ] }, { "page": "hapdos2mrkdos", "title": "calculate the marker dosages resulting from haplotype dosage combinations", "topics": [ "hapdos2mrkdos" ] }, { "page": "haploblock_df2list", "title": "convert a haploblock-defining data frame to a list", "topics": [ "haploblock_df2list" ] }, { "page": "inferHaplotypes", "title": "infer haplotypes for one or more haploblocks", "topics": [ "inferHaplotypes" ] }, { "page": "make.Happyinf.input", "title": "convert PolyHaplotyper input data to Happy-inf format", "topics": [ "make.Happyinf.input" ] }, { "page": "make.SATlotyper.input", "title": "convert PolyHaplotyper marker data to SATlotyper format", "topics": [ "make.SATlotyper.input" ] }, { "page": "make.ShesisPlus.input", "title": "convert PolyHaplotyper marker data to ShesisPlus format", "topics": [ "make.ShesisPlus.input" ] }, { "page": "mergeReplicates", "title": "merge replicate samples in dosage matrix", "topics": [ "mergeReplicates" ] }, { "page": "mrkdid2mrkdos", "title": "get the marker dosages from mrkdids (marker dosage IDs)", "topics": [ "mrkdid2mrkdos" ] }, { "page": "mrkdos2mrkdid", "title": "get marker dosage IDs from marker dosages", "topics": [ "mrkdos2mrkdid" ] }, { "page": "overviewByFS", "title": "generate an overview of the results by haploblock and by FS family", "topics": [ "overviewByFS" ] }, { "page": "padded", "title": "pad an integer (prefix with zeroes to a fixed length)", "topics": [ "padded" ] }, { "page": "pedigreeHapCheck", "title": "check the consistency of haploblock genotypes over a pedigree", "topics": [ "pedigreeHapCheck" ] }, { "page": "pedigreeSim2PH", "title": "convert the PedigreeSim true haplotypes to marker dosages and haplotype dosages", "topics": [ "pedigreeSim2PH" ] }, { "page": "phblocks", "title": "List of markers per haploblock", "topics": [ "phblocks" ] }, { "page": "phdos", "title": "dosages of SNP alleles", "topics": [ "phdos" ] }, { "page": "phFS", "title": "members of FS families", "topics": [ "phFS" ] }, { "page": "phpar", "title": "parents of FS families", "topics": [ "phpar" ] }, { "page": "phped", "title": "pedigree", "topics": [ "phped" ] }, { "page": "phresults", "title": "haplotyping results", "topics": [ "phresults" ] }, { "page": "read.Happyinf.output", "title": "read the haplotyping results from the Happy-inf output", "topics": [ "read.Happyinf.output" ] }, { "page": "read.SATlotyper.output", "title": "read the haplotyping results from the SATlotyper output", "topics": [ "read.SATlotyper.output" ] }, { "page": "read.ShesisPlus.output", "title": "Read the haplotyping results from the ShesisPlus output", "topics": [ "read.ShesisPlus.output" ] }, { "page": "run.SATlotyper", "title": "A simple interface to run SATlotyper", "topics": [ "run.SATlotyper" ] }, { "page": "showOneFS", "title": "show marker and haplotype dosages for one FS family", "topics": [ "showOneFS" ] }, { "page": "totHapcombCount", "title": "calculate the total nr of possible haplotype combinations", "topics": [ "totHapcombCount" ] }, { "page": "usedhap", "title": "Find all used (inferred) haplotypes", "topics": [ "usedhap" ] } ], "_rundeps": [ "XML" ], "_vignettes": [ { "source": "PolyHaplotyper.Rmd", "filename": "PolyHaplotyper.html", "title": "PolyHaplotyper vignette", "author": "Roeland E. Voorrips", "engine": "knitr::rmarkdown", "headings": [ "PolyHaplotyper vignette", "Roeland E. Voorrips, r Sys.Date()", "Input data", "Haploblock definitions", "Marker data", "Pedigree", "FS families", "Haplotyping", "Overviews and statistics", "Overviews by FS family", "Pedigree check", "Summary statistics", "Number of markers vs number of haplotypes", "Segregation in one FS, one haploblock", "Remarks" ], "created": "2021-02-10 09:40:32", "modified": "2021-02-10 09:40:32", "commits": 1 } ], "_score": 2, "_indexed": true, "_nocasepkg": "polyhaplotyper", "_universes": [ "roelandv" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "1.0.1", "date": "2026-05-07T05:38:07.000Z", "distro": "noble", "commit": "c733cbb69263b2e96635d805bc22c77183d734ef", "fileid": "b865deb39e2f875f4c1909938da06896aec116e819d6b436e7c635a5def345a1", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/roelandv/actions/runs/25477838344" }, { "r": "4.6.0", "os": "linux", "version": "1.0.1", "date": "2026-05-07T05:38:23.000Z", "distro": "noble", "commit": "c733cbb69263b2e96635d805bc22c77183d734ef", "fileid": "82da16f69cabd162decbc7977d51cae84c3ff6edbb40ce7564a63fab241d9b7f", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/roelandv/actions/runs/25477838344" }, { "r": "4.5.3", "os": "mac", "version": "1.0.1", "date": "2026-05-07T05:38:33.000Z", "commit": "c733cbb69263b2e96635d805bc22c77183d734ef", "fileid": "0055fe244dca33ff4dfc2f50e3e0d63cd97b4fd7cb653b95da5c4c9a9556cb20", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/roelandv/actions/runs/25477838344" }, { "r": "4.6.0", "os": "mac", "version": "1.0.1", "date": "2026-05-07T05:37:54.000Z", "commit": "c733cbb69263b2e96635d805bc22c77183d734ef", "fileid": "655399a6b99a88ed3be943014a8afd84c8a4b6f1118dc30643c3ce0ff9608c14", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/roelandv/actions/runs/25477838344" }, { "r": "4.7.0", "os": "win", "version": "1.0.1", "date": "2026-05-07T05:37:15.000Z", "commit": "c733cbb69263b2e96635d805bc22c77183d734ef", "fileid": "dae8900775ac9fdba009bc7f0ee5c40743d3b3a52be5a865b7b20efcddd40374", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/roelandv/actions/runs/25477838344" }, { "r": "4.5.3", "os": "win", "version": "1.0.1", "date": "2026-05-07T05:37:52.000Z", "commit": "c733cbb69263b2e96635d805bc22c77183d734ef", "fileid": "4f8fade9be3410128a7dd903993865cac5ff3183639f8cc42accd9b413814bfb", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/roelandv/actions/runs/25477838344" }, { "r": "4.6.0", "os": "win", "version": "1.0.1", "date": "2026-05-07T05:37:09.000Z", "commit": "c733cbb69263b2e96635d805bc22c77183d734ef", "fileid": "9664747c51d02a3f45a2eefb35c61cc466cce73e42347ac7a6796e64acf4a73d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/roelandv/actions/runs/25477838344" }, { "r": "4.6.0", "os": "wasm", "version": "1.0.1", "date": "2026-05-22T15:20:41.000Z", "commit": "c733cbb69263b2e96635d805bc22c77183d734ef", "fileid": "181fcc11e708c290167bf5aabeb951d461625c2423056f545708864f2ef2fe9a", "status": "success", "buildurl": "https://github.com/r-universe/roelandv/actions/runs/25477838344" } ] }