Package: qtlpoly 0.2.4

Gabriel de Siqueira Gesteira

qtlpoly: Random-Effect Multiple QTL Mapping in Autopolyploids

Performs random-effect multiple interval mapping (REMIM) in full-sib families of autopolyploid species based on restricted maximum likelihood (REML) estimation and score statistics, as described in Pereira et al. (2020) <doi:10.1534/genetics.120.303080>.

Authors:Guilherme da Silva Pereira [aut], Marcelo Mollinari [ctb], Gabriel de Siqueira Gesteira [ctb, cre], Zhao-Bang Zeng [ctb], Long Qu [ctb], Giovanny Covarrubias-Pazaran [ctb]

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

# Install 'qtlpoly' in R:
install.packages('qtlpoly', repos = c('https://polyploids.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/gabrielgesteira/qtlpoly/issues

Uses libs:
  • openblas– Optimized BLAS
  • c++– GNU Standard C++ Library v3
  • openmp– GCC OpenMP (GOMP) support library
Datasets:
  • B2721 - Autotetraploid potato dataset
  • hexafake - Simulated autohexaploid dataset.
  • maps4x - Autotetraploid potato map
  • maps6x - Simulated autohexaploid map
  • pheno4x - Autotetraploid potato phenotypes
  • pheno6x - Simulated phenotypes

On CRAN:

polyploidqtl-mapping

5.33 score 6 stars 60 scripts 224 downloads 1 mentions 20 exports 171 dependencies

Last updated 5 days agofrom:96e99f0300. Checks:OK: 9. Indexed: no.

TargetResultDate
Doc / VignettesOKNov 14 2024
R-4.5-win-x86_64OKNov 14 2024
R-4.5-linux-x86_64OKNov 14 2024
R-4.4-win-x86_64OKNov 14 2024
R-4.4-mac-x86_64OKNov 14 2024
R-4.4-mac-aarch64OKNov 14 2024
R-4.3-win-x86_64OKNov 14 2024
R-4.3-mac-x86_64OKNov 14 2024
R-4.3-mac-aarch64OKNov 14 2024

Exports:breeding_valuesfeimfit_modelfit_model2modify_qtlnull_modelnull_model2optimize_qtlpermutationsplot_profileplot_qtlplot_sintprofile_qtlqtl_effectsread_dataread_data2remimremim2search_qtlsimulate_qtl

Dependencies:abindapeaskpassbackportsbase64encbitbit64bitopsbootbroombslibcachemcarcarDatacheckmateclassclicliprclustercodetoolscolorspaceCompQuadFormcorrplotcowplotcpp11crayoncrosstalkcurldata.tabledendextendDerivdigestdoBydoParalleldotCall64dplyre1071ellipseevaluatefansifarverfastmapfieldsfontawesomeforcatsforeachforeignFormulafsgdatagenericsggplot2ggpubrggrepelggsciggsignifglmnetgluegridExtragtablegtoolshavenhighrHmischmshtmlTablehtmltoolshtmlwidgetshttrisobanditeratorsjomojquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4magrittrmappolymapsMASSMatrixMatrixModelsmemoisememusemgcvmicemicrobenchmarkmimeminqamisc3dmitmlmodelrmunsellmvtnormnlmenloptrnnetnnlsnumDerivopensslordinalpanpbkrtestpermutepillarpinfsc50pkgconfigplot3DplotlyplotrixplyrpolynomprettyunitsprincurveprogresspromisesproxypurrrquadprogquantregR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRcppProgressRCurlreadrreshape2rlangRLRsimrmarkdownrpartrstatixrstudioapisassscalesshapesmacofspamSparseMstringistringrsurvivalsystibbletidyrtidyselecttinytextzdbucminfutf8vcfRvctrsveganviridisviridisLitevroomweightswithrwordcloudxfunyamlzoo