Package: fitPoly 4.0.0

fitPoly: Genotype Calling for Bi-Allelic Marker Assays

Genotyping assays for bi-allelic markers (e.g. SNPs) produce signal intensities for the two alleles. 'fitPoly' assigns genotypes (allele dosages) to a collection of polyploid samples based on these signal intensities. 'fitPoly' replaces the older package 'fitTetra' that was limited (a.o.) to only tetraploid populations whereas 'fitPoly' accepts any ploidy level. Reference: Voorrips RE, Gort G, Vosman B (2011) <doi:10.1186/1471-2105-12-172>. New functions added on conversion of data from SNP array software formats, drawing of XY-scatterplots with or without genotype colors, checking against expected F1 segregation patterns, comparing results from two different assays (probes) for the same SNP, recovery from a saveMarkerModels() crash.

Authors:Roeland E. Voorrips [aut], Gerrit Gort [aut], Alejandro Therese Navarro [aut], Giorgio Tumino [aut, cre]

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fitPoly.pdf |fitPoly.html✨
fitPoly/json (API)

# Install 'fitPoly' in R:
install.packages('fitPoly', repos = c('https://gitumino.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • XYdat - A data set containing SNP array data
  • fitPoly_data - Small fitPoly input datasets for testing and examples
  • scores - A data set with dosage scores generated by fitPoly

On CRAN:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

4.13 score 15 scripts 238 downloads 9 mentions 36 exports 5 dependencies

Last updated 7 days agofrom:34eb841bf2. Checks:8 OK. Indexed: yes.

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Doc / VignettesOKFeb 14 2025
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R-4.5-linuxOKFeb 14 2025
R-4.4-winOKFeb 16 2025
R-4.4-macOKFeb 14 2025
R-4.3-winOKFeb 14 2025
R-4.3-macOKFeb 14 2025

Exports:calcRstatscalcSegtypeInfocheckF1checkFilenameCodomMarkercombineFilescompareProbesconcatbatchconvertStartmeanscorrectDosagesdrawXYplotsexpandUnknownParentsF1Dosages2MatrixfitMarkersfitOneMarkerget.genocolgetBatchFilesleftstrlistSegtypesmakeFitPolyFilesreadAxiomSummaryreadDatfilereadFullDataTableremoveRedundantrightstrsamplestatssaveMarkerModelsscores2widesegtypeInfoSummaryselMarkers_byRselMarkers_qallselSegtypeInfosplitNrenameSampleswriteDatfilewriteDosagefileXY_plot

Dependencies:codetoolsdevEMFdoParallelforeachiterators

Analysis of F1 scores

Roeland E. Voorrips, Alejandro Therese Navarro

Rendered fromSegregation_analysis_of_dosage_scores.Rmdusingknitr::rmarkdownon Feb 14 2025.

Last update: 2025-02-13
Started: 2025-02-13

Data import and preparation

Roeland E. Voorrips, Alejandro Therese Navarro

Rendered fromData_import_and_preparation.Rmdusingknitr::rmarkdownon Feb 14 2025.

Last update: 2025-02-13
Started: 2025-02-13

Readme and manuals

Help Manual

Help pageTopics
Calculate statistics of R per markercalcRstats
Build a list of segregation typescalcSegtypeInfo
Identify the best-fitting F1 segregation typescheckF1
Check if a file can be createdcheckFilename
Function to fit a multiple mixture model to a vector of signal ratios of a single bi-allelic markerCodomMarker
Combine the X and Y intensity scores and the assigned dosage in one filecombineFiles
Compare and combine results from two probes for the same SNPcompareProbes
Construct the log, models and scores files from a set of batch filesconcatbatch
A function to convert a set of mixture means from one ploidy to anotherconvertStartmeans
Check if dosage scores may have to be shiftedcorrectDosages
Draws a series of pages, each with 6 XY-plots showing allele signals and assigned dosagesdrawXYplots
Generate markers with all combinations of parental scoresexpandUnknownParents
Convert the F1 dosage scores data.frame or file to polymapR input matrixF1Dosages2Matrix
Function to fit mixture models for series of markers and save the results to filesfitMarkers
Function to fit multiple mixture models to signal ratios of a single bi-allelic markerfitOneMarker
fitPoly: a package for assigning dosage scores based on SNP array datafitPoly-package fitPoly
Small fitPoly input datasets for testing and examplesfitPoly_data
fitPolyTools: a package with functions related to package fitPolyfitPolyTools
Generate a set of genotype (dosage) colors for XY-plotsget.genocol
get the names of all batch files presentgetBatchFiles
Get substrings from the lefthand sideleftstr
conversion of segtype code to F1 segregation ratioslistSegtypes
Make input files for fitPoly containing only selected rows and columnsmakeFitPolyFiles
convert an Affymetrix AxiomCT1.summary file to the import format for fitPolyreadAxiomSummary
User-friendly wrapper for read.tablereadDatfile
convert a GenomeStudio FullDataTable file to the import format for fitPolyreadFullDataTable
Remove redundant single-probe markersremoveRedundant
Get substrings from the righthand siderightstr
Statistics for each F1 sample over all markerssamplestats
DEPRECATED: Function to fit mixture models for series of markers and save the results to filessaveMarkerModels
A data set with dosage scores generated by fitPolyscores
Convert a scores file from long to wide formatscores2wide
Summarize the segtypeInfo listsegtypeInfoSummary
Select markers at specified R levelsselMarkers_byR
Sample markers at several qall levelsselMarkers_qall
Restrict a list of segregation types to specified inheritance modesselSegtypeInfo
Rename samples from array codes to user codes, and split diploid from polyploid samplessplitNrenameSamples
User-friendly wrapper for write.tablewriteDatfile
Write a file with segregation types and dosage scoreswriteDosagefile
Draws an XY-plot showing allele signals and assigned dosagesXY_plot
A data set containing SNP array dataXYdat