{ "_id": "6aae468c3d719c1f8407a8ad", "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": "2026-09-19 08:20:23 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", "_user": "gitumino", "_type": "src", "_file": "fitPoly_4.0.0.tar.gz", "_fileid": "https://r2.ropensci.org/cdfdb7146a8be9973712845b3faca1b679012fa9e3b4aaa0d258dbe8ae36ba6b", "_filesize": 1855672, "_sha256": "cdfdb7146a8be9973712845b3faca1b679012fa9e3b4aaa0d258dbe8ae36ba6b", "_expires": "2026-12-28T08:23:38.000Z", "_created": "2026-09-19T08:20:23.000Z", "_published": "2026-09-19T08:23:39.973Z", "_jobs": [ { "job": 105867490969, "time": 134, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "OK", "artifact": "10580923640" }, { "job": 105867490977, "time": 134, "config": 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"uuid": 92988320 }, { "user": "roelandv", "count": 1, "uuid": 1846618 } ], "_userbio": { "uuid": 92988320, "type": "user", "name": "gitumino", "followers": 0 }, "_downloads": { "count": 310, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/fitPoly" }, "_mentions": 9, "_searchresults": 25, "_rbuild": "4.6.1", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/fitPoly.html", "extra/manual.pdf", "extra/readme.html", "extra/readme.md" ], "_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. 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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": 4.352182518111363, "_indexed": true, "_nocasepkg": "fitpoly", "_universes": [ "gitumino" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "4.0.0", "date": "2026-09-19T08:22:36.000Z", "distro": "resolute", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "https://r2.ropensci.org/2c090ebe4aa856003ef70bf3e282797b6645bd5c6450bc54e5ea14e470533ba2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/35431545599" }, { "r": "4.6.1", "os": "linux", "version": "4.0.0", "date": "2026-09-19T08:22:38.000Z", "distro": "resolute", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "https://r2.ropensci.org/1b356d52d9238838773f36d363ea7238c287d1e550fde644cc56e16d38e08202", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/35431545599" }, { "r": "4.5.3", "os": "mac", "version": "4.0.0", "date": "2026-09-19T08:22:26.000Z", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "https://r2.ropensci.org/1d9b68fb5ff2dcf5c4c6bd0f4928989cc174b318674411861abf9ee5300a7e40", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/35431545599" }, { "r": "4.6.1", "os": "mac", "version": "4.0.0", "date": "2026-09-19T08:22:14.000Z", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "https://r2.ropensci.org/fed2790a02bf43cf3fb81d9948080dda99c3b737ea6937f07b8f36daf33eb1f2", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/35431545599" }, { "r": "4.6.0", "os": "wasm", "version": "4.0.0", "date": "2026-09-19T08:22:35.000Z", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "https://r2.ropensci.org/3cbc1fee6eba6c062c902566abb0a4047a833534420d60d4c6798880e7f2a358", "status": "success", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/35431545599" }, { "r": "4.7.0", "os": "win", "version": "4.0.0", "date": "2026-09-19T08:21:55.000Z", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "https://r2.ropensci.org/8b28799940a93ed027653f550dfacf20d729a6746c6d95022d94dd6c56e88df0", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/35431545599" }, { "r": "4.5.3", "os": "win", "version": "4.0.0", "date": "2026-09-19T08:21:28.000Z", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "https://r2.ropensci.org/c026f63afabe62cd94722fb0d079824d416bb4ccf3b9dca5601f97d140134e26", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/35431545599" }, { "r": "4.6.1", "os": "win", "version": "4.0.0", "date": "2026-09-19T08:21:41.000Z", "commit": "34eb841bf25908f32c58203bd5c0d57400adf1cf", "fileid": "https://r2.ropensci.org/f2d5c83b13cf018a6af4db6cf50ca757e4ae28c221d7ef863066382468df01fe", "status": "success", "check": "OK", "buildurl": "https://github.com/r-universe/gitumino/actions/runs/35431545599" } ] }