{ "_id": "6a1f06aab401979e7341bc85", "Package": "fitPoly", "Type": "Package", "Title": "Genotype Calling for Bi-Allelic Marker Assays", "Version": "4.0.0", "Date": "2025-02-10", "Authors@R": "c(person(given = c(\"Roeland\", \"E.\"),\nfamily = \"Voorrips\",\nrole = \"aut\"),\nperson(given = \"Gerrit\",\nfamily = \"Gort\",\nrole = \"aut\"),\nperson(given = c(\"Alejandro\"),\nfamily = \"Therese Navarro\",\nrole = \"aut\"),\nperson(given = \"Giorgio\",\nfamily = \"Tumino\",\nrole = c(\"aut\", \"cre\"),\nemail = \"giorgio.tumino@wur.nl\"))", "Description": "Genotyping assays for bi-allelic markers (e.g. SNPs)\nproduce signal intensities for the two alleles. 'fitPoly'\nassigns genotypes (allele dosages) to a collection of polyploid\nsamples based on these signal intensities. 'fitPoly' replaces\nthe older package 'fitTetra' that was limited (a.o.) to only\ntetraploid populations whereas 'fitPoly' accepts any ploidy\nlevel. Reference: Voorrips RE, Gort G, Vosman B (2011)\n. New functions added on\nconversion of data from SNP array software formats, drawing of\nXY-scatterplots with or without genotype colors, checking\nagainst expected F1 segregation patterns, comparing results\nfrom two different assays (probes) for the same SNP, recovery\nfrom a saveMarkerModels() crash.", "License": "GPL-2", "RoxygenNote": "7.3.1", "VignetteBuilder": "knitr", "NeedsCompilation": "no", "Encoding": "UTF-8", "Packaged": { "Date": "2026-05-18 07:01:17 UTC", "User": "root" }, "Author": "Roeland E. Voorrips [aut], Gerrit Gort [aut], Alejandro Therese\nNavarro [aut], Giorgio Tumino [aut, cre]", "Maintainer": "Giorgio Tumino ", "Config/pak/sysreqs": "libfontconfig1-dev zlib1g-dev", "Repository": "https://gitumino.r-universe.dev", "Date/Publication": "2025-02-13 12:42:05 UTC", "RemoteUrl": "https://github.com/cran/fitPoly", "RemoteRef": "HEAD", "RemoteSha": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "MD5sum": "f052e23f01d5373844b6235eeab8ee69", "_user": "gitumino", "_type": "src", "_file": "fitPoly_4.0.0.tar.gz", "_fileid": "207a8f608a93c950a7d15ff21796dce777420d10ff17d81aae7788adf7e9b32f", "_filesize": 1855780, "_sha256": "207a8f608a93c950a7d15ff21796dce777420d10ff17d81aae7788adf7e9b32f", "_created": "2026-05-18T07:01:17.000Z", "_published": "2026-06-02T16:36:58.896Z", "_distro": "noble", "_jobs": [ { "job": 79122191707, "time": 140, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "7051409880" }, { "job": 79122192077, "time": 142, "config": 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"_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/cran/fitPoly", "_commit": { "id": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "author": "Giorgio Tumino ", "committer": "cran-robot ", "message": "version 4.0.0\n", "time": 1739450525 }, "_maintainer": { "name": "Giorgio Tumino", "email": "giorgio.tumino@wur.nl", "login": "gitumino", "description": "", "uuid": 92988320 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.2.0", "role": "Depends" }, { "package": "foreach", "role": "Imports" }, { "package": "devEMF", "role": "Imports" }, { "package": "doParallel", "role": "Imports" }, { "package": "grDevices", "role": "Imports" }, { "package": "knitr", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" } ], "_owner": "cran", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_stars": 0, "_contributors": [ { "user": "gitumino", "count": 1, "uuid": 92988320 }, { "user": "roelandv", "count": 1, "uuid": 1846618 } ], "_userbio": { "uuid": 92988320, "type": "user", "name": "gitumino" }, "_downloads": { "count": 247, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/fitPoly" }, "_searchresults": 20, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/fitPoly.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_realowner": "gitumino", "_cranurl": false, "_releases": [ { "version": "3.0.0", "date": "2018-03-16" }, { "version": "4.0.0", "date": "2025-02-13" } ], "_exports": [ "calcRstats", "calcSegtypeInfo", "checkF1", "checkFilename", "CodomMarker", "combineFiles", "compareProbes", "concatbatch", "convertStartmeans", "correctDosages", "drawXYplots", "expandUnknownParents", "F1Dosages2Matrix", "fitMarkers", "fitOneMarker", "get.genocol", "getBatchFiles", "leftstr", "listSegtypes", "makeFitPolyFiles", "readAxiomSummary", "readDatfile", "readFullDataTable", "removeRedundant", "rightstr", "samplestats", "saveMarkerModels", "scores2wide", "segtypeInfoSummary", "selMarkers_byR", "selMarkers_qall", "selSegtypeInfo", "splitNrenameSamples", "writeDatfile", "writeDosagefile", "XY_plot" ], "_datasets": [ { "name": "fitPoly_data", "title": "Small fitPoly input datasets for testing and examples", "object": "fitPoly_data", "file": "fitPoly_data.RData", "class": [ "list" ], "fields": [], "table": false, "tojson": true }, { "name": "scores", "title": "A data set with dosage scores generated by fitPoly", "object": "scores", "file": "scores.RData", "class": [ "data.frame" ], "fields": [ "marker", "MarkerName", "SampleName", "ratio", "P0", "P1", "P2", "P3", "P4", "maxgeno", "maxP", "geno" ], "rows": 17013, "table": true, "tojson": true }, { "name": "XYdat", "title": "A data set containing SNP array data", "object": "XYdat", "file": "XYdat.RData", "class": [ "data.frame" ], "fields": [ "MarkerName", "SampleName", "X", "Y", "R", "ratio" ], "rows": 17808, "table": true, "tojson": true } ], "_help": [ { "page": "calcRstats", "title": "Calculate statistics of R per marker", "topics": [ "calcRstats" ] }, { "page": "calcSegtypeInfo", "title": "Build a list of segregation types", "topics": [ "calcSegtypeInfo" ] }, { "page": "checkF1", "title": "Identify the best-fitting F1 segregation types", "topics": [ "checkF1" ] }, { "page": "checkFilename", "title": "Check if a file can be created", "topics": [ "checkFilename" ] }, { "page": "CodomMarker", "title": "Function to fit a multiple mixture model to a vector of signal ratios of a single bi-allelic marker", "topics": [ "CodomMarker" ] }, { "page": "combineFiles", "title": "Combine the X and Y intensity scores and the assigned dosage in one file", "topics": [ "combineFiles" ] }, { "page": "compareProbes", "title": "Compare and combine results from two probes for the same SNP", "topics": [ "compareProbes" ] }, { "page": "concatbatch", "title": "Construct the log, models and scores files from a set of batch files", "topics": [ "concatbatch" ] }, { "page": "convertStartmeans", "title": "A function to convert a set of mixture means from one ploidy to another", "topics": [ "convertStartmeans" ] }, { "page": "correctDosages", "title": "Check if dosage scores may have to be shifted", "topics": [ "correctDosages" ] }, { "page": "drawXYplots", "title": "Draws a series of pages, each with 6 XY-plots showing allele signals and assigned dosages", "topics": [ "drawXYplots" ] }, { "page": "expandUnknownParents", "title": "Generate markers with all combinations of parental scores", "topics": [ "expandUnknownParents" ] }, { "page": "F1Dosages2Matrix", "title": "Convert the F1 dosage scores data.frame or file to polymapR input matrix", "topics": [ "F1Dosages2Matrix" ] }, { "page": "fitMarkers", "title": "Function to fit mixture models for series of markers and save the results to files", "topics": [ "fitMarkers" ] }, { "page": "fitOneMarker", "title": "Function to fit multiple mixture models to signal ratios of a single bi-allelic marker", "topics": [ "fitOneMarker" ] }, { "page": "fitPoly", "title": "fitPoly: a package for assigning dosage scores based on SNP array data", "topics": [ "fitPoly-package", "fitPoly" ] }, { "page": "fitPoly_data", "title": "Small fitPoly input datasets for testing and examples", "topics": [ "fitPoly_data" ] }, { "page": "fitPolyTools", "title": "fitPolyTools: a package with functions related to package fitPoly", "topics": [ "fitPolyTools" ] }, { "page": "get.genocol", "title": "Generate a set of genotype (dosage) colors for XY-plots", "topics": [ "get.genocol" ] }, { "page": "getBatchFiles", "title": "get the names of all batch files present", "topics": [ "getBatchFiles" ] }, { "page": "leftstr", "title": "Get substrings from the lefthand side", "topics": [ "leftstr" ] }, { "page": "listSegtypes", "title": "conversion of segtype code to F1 segregation ratios", "topics": [ "listSegtypes" ] }, { "page": "makeFitPolyFiles", "title": "Make input files for fitPoly containing only selected rows and columns", "topics": [ "makeFitPolyFiles" ] }, { "page": "readAxiomSummary", "title": "convert an Affymetrix AxiomCT1.summary file to the import format for fitPoly", "topics": [ "readAxiomSummary" ] }, { "page": "readDatfile", "title": "User-friendly wrapper for read.table", "topics": [ "readDatfile" ] }, { "page": "readFullDataTable", "title": "convert a GenomeStudio FullDataTable file to the import format for fitPoly", "topics": [ "readFullDataTable" ] }, { "page": "removeRedundant", "title": "Remove redundant single-probe markers", "topics": [ "removeRedundant" ] }, { "page": "rightstr", "title": "Get substrings from the righthand side", "topics": [ "rightstr" ] }, { "page": "samplestats", "title": "Statistics for each F1 sample over all markers", "topics": [ "samplestats" ] }, { "page": "saveMarkerModels", "title": "DEPRECATED: Function to fit mixture models for series of markers and save the results to files", "topics": [ "saveMarkerModels" ] }, { "page": "scores", "title": "A data set with dosage scores generated by fitPoly", "topics": [ "scores" ] }, { "page": "scores2wide", "title": "Convert a scores file from long to wide format", "topics": [ "scores2wide" ] }, { "page": "segtypeInfoSummary", "title": "Summarize the segtypeInfo list", "topics": [ "segtypeInfoSummary" ] }, { "page": "selMarkers_byR", "title": "Select markers at specified R levels", "topics": [ "selMarkers_byR" ] }, { "page": "selMarkers_qall", "title": "Sample markers at several qall levels", "topics": [ "selMarkers_qall" ] }, { "page": "selSegtypeInfo", "title": "Restrict a list of segregation types to specified inheritance modes", "topics": [ "selSegtypeInfo" ] }, { "page": "splitNrenameSamples", "title": "Rename samples from array codes to user codes, and split diploid from polyploid samples", "topics": [ "splitNrenameSamples" ] }, { "page": "writeDatfile", "title": "User-friendly wrapper for write.table", "topics": [ "writeDatfile" ] }, { "page": "writeDosagefile", "title": "Write a file with segregation types and dosage scores", "topics": [ "writeDosagefile" ] }, { "page": "XY_plot", "title": "Draws an XY-plot showing allele signals and assigned dosages", "topics": [ "XY_plot" ] }, { "page": "XYdat", "title": "A data set containing SNP array data", "topics": [ "XYdat" ] } ], "_readme": "https://github.com/cran/fitPoly/raw/HEAD/README.md", "_rundeps": [ "codetools", "devEMF", "doParallel", "foreach", "iterators" ], "_vignettes": [ { "source": "Segregation_analysis_of_dosage_scores.Rmd", "filename": "Segregation_analysis_of_dosage_scores.html", "title": "Analysis of F1 scores", "author": "Roeland E. Voorrips, Alejandro Therese Navarro", "engine": "knitr::rmarkdown", "headings": [ "Exercise 1: Segregation types and quality", "Exercise 2: checking for \"shifted\" markers", "Exercise 3: select acceptably scored markers", "Exercise 4: combine probes" ], "created": "2025-02-13 12:42:05", "modified": "2025-02-13 12:42:05", "commits": 1 }, { "source": "Data_import_and_preparation.Rmd", "filename": "Data_import_and_preparation.html", "title": "Data import and preparation", "author": "Roeland E. Voorrips, Alejandro Therese Navarro", "engine": "knitr::rmarkdown", "headings": [ "Exercise 1: extract data from SNP array", "Illumina", "Affymetrix", "Read and convert the array data", "Exercise 2: Rename the samples and separate by ploidy level", "Exercise 3: Filtering the data based on total signal intensity", "3a: Selection of samples based on total signal intensity", "3b: Selection of markers based on total signal intensity", "3c: Selection based on R values of samples within markers", "Excersise 4: run fitPoly" ], "created": "2025-02-13 12:42:05", "modified": "2025-02-13 12:42:05", "commits": 1 } ], "_score": 3.3010299956639813, "_indexed": true, "_nocasepkg": "fitpoly", "_universes": [ "gitumino" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "4.0.0", "date": "2026-05-18T07:03:31.000Z", "distro": "noble", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "88d303f6cd65ba680824abeddb73dd6f63aaf682d7104d272f5cbd5033a6dd42", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/26018433268" }, { "r": "4.6.0", "os": "linux", "version": "4.0.0", "date": "2026-05-18T07:03:31.000Z", "distro": "noble", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "a23edb4858bd7fd0958cee82929e5a068b44e0d83a3e2f19f33d311200ea2225", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/26018433268" }, { "r": "4.5.3", "os": "mac", "version": "4.0.0", "date": "2026-05-18T07:04:19.000Z", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "d59ca1e2b04f362909fb12954d14b8deac725c6b76caf05d3777b79b8d0dc1b3", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/26018433268" }, { "r": "4.6.0", "os": "mac", "version": "4.0.0", "date": "2026-05-18T07:05:14.000Z", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "dfff02e92de518b1e4576046a7835b73c4c6c9d8a2bd4ffd3c67b592b9a6f26d", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/26018433268" }, { "r": "4.7.0", "os": "win", "version": "4.0.0", "date": "2026-05-18T07:02:51.000Z", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "8b96708e0c10bc1bb8fbe60904edff0c4575de9345c54becc01760a4a3609c04", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/26018433268" }, { "r": "4.5.3", "os": "win", "version": "4.0.0", "date": "2026-05-18T07:02:25.000Z", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "0ae2c65e90588e4083e31411d19eb04a04085b3ed21e9847ecaab9a0938b4bc2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/26018433268" }, { "r": "4.6.0", "os": "win", "version": "4.0.0", "date": "2026-05-18T07:02:19.000Z", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "9be1b9d5b92397999628d384bbbc2f45d5edced1709ed80e160fc2f49e8ef88c", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/26018433268" }, { "r": "4.6.0", "os": "wasm", "version": "4.0.0", "date": "2026-06-02T16:36:37.000Z", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "fe4b70b82024025c08aecaea5b7ff9c80f235c33adcdb995e89f43fd7a646d47", "status": "success", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/26018433268" } ] }