Package: polyqtlR 0.1.1
polyqtlR: QTL Analysis in Autopolyploid Bi-Parental F1 Populations
Quantitative trait loci (QTL) analysis and exploration of meiotic patterns in autopolyploid bi-parental F1 populations. For all ploidy levels, identity-by-descent (IBD) probabilities can be estimated. Significance thresholds, exploring QTL allele effects and visualising results are provided. For more background and to reference the package see <doi:10.1093/bioinformatics/btab574>.
Authors:
polyqtlR_0.1.1.tar.gz
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polyqtlR.pdf |polyqtlR.html✨
polyqtlR/json (API)
# Install 'polyqtlR' in R: |
install.packages('polyqtlR', repos = c('https://polyploids.r-universe.dev', 'https://cloud.r-project.org')) |
- BLUEs.pheno - Best Linear Unbiased Estimates of phenotype
- GIC_4x - Genotypic Information Coefficient for example tetraploid
- IBD_4x - Identical by descent probabilities for example tetraploid
- Phenotypes_4x - Phenotypes for example tetraploid
- Rec_Data_4x - Recombination data for example tetraploid
- SNP_dosages.4x - SNP marker dosage data for example tetraploid
- mr.ls - Example output of meiosis report function
- phased_maplist.4x - Phased maplist for example tetraploid
- qtl_LODs.4x - QTL output for example tetraploid
- segList_2x - Expected segregation for all markers types of a diploid cross
- segList_3x - Expected segregation for all markers types of a triploid cross
- segList_3x_24 - Expected segregation for all markers types of a triploid cross
- segList_4x - Expected segregation for all markers types of a tetraploid cross
- segList_6x - Expected segregation for all markers types of a hexaploid cross
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 11 months agofrom:a7317b59cc. Checks:OK: 9. Indexed: no.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 02 2024 |
R-4.5-win-x86_64 | OK | Nov 02 2024 |
R-4.5-linux-x86_64 | OK | Nov 02 2024 |
R-4.4-win-x86_64 | OK | Nov 02 2024 |
R-4.4-mac-x86_64 | OK | Nov 02 2024 |
R-4.4-mac-aarch64 | OK | Nov 02 2024 |
R-4.3-win-x86_64 | OK | Nov 02 2024 |
R-4.3-mac-x86_64 | OK | Nov 02 2024 |
R-4.3-mac-aarch64 | OK | Nov 02 2024 |
Exports:BLUEcheck_cofactorsconvert_mappoly_to_phased.maplistcount_recombinationsestimate_GICestimate_IBDexploreQTLfindPeakfindSupportimport_IBDimpute_dosagesmaxL_IBDmeiosis_reportplotLinearQTLplotLinearQTL_listplotQTLplotRecLSPVEQTLscansegMakersingleMarkerRegressionspline_IBDthinmapvisualiseGICvisualiseHaplovisualisePairingvisualiseQTLeffects
Dependencies:abindbackportsbase64encbslibcachemcheckmatecliclustercodetoolscolorspacedata.tabledigestdoParallelevaluatefansifarverfastmapfontawesomeforeachforeignFormulafsggplot2gluegridExtragtablehighrHmischtmlTablehtmltoolshtmlwidgetsisobanditeratorsjquerylibjsonliteknitrlabelinglatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmennetpillarpkgconfigplyrR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangrmarkdownrpartrstudioapisassscalesstringistringrtibbletinytexutf8vctrsviridisviridisLitewithrxfunyaml