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

20 exports 5 stars 1.69 score 183 dependencies

Last updated 3 months agofrom:2578b3570bd3653521b7e1d712039296820b72f7

Exports:breeding_valuesfeimfit_modelfit_model2modify_qtlnull_modelnull_model2optimize_qtlpermutationsplot_profileplot_qtlplot_sintprofile_qtlqtl_effectsread_dataread_data2remimremim2search_qtlsimulate_qtl

Dependencies:abindapeaskpassbackportsbase64encbitbit64bitopsbootbriobroombslibcachemcallrcandisccarcarDatacheckmateclassclicliprclustercodetoolscolorspaceCompQuadFormcorrplotcowplotcpp11crayoncrosstalkcurldata.tabledendextenddescdiffobjdigestdoParalleldotCall64dplyre1071ellipseevaluatefansifarverfastmapfieldsfontawesomeforcatsforeachforeignFormulafsgdatagenericsggplot2ggpubrggrepelggsciggsignifglmnetgluegridExtragtablegtoolshavenheplotshighrHmischmshtmlTablehtmltoolshtmlwidgetshttrisobanditeratorsjomojquerylibjsonliteknitrlabelinglaterlatticelazyevallifecyclelme4magrittrmappolymapsMASSMatrixMatrixModelsmemoisememusemgcvmicemimeminqamisc3dmitmlmunsellmvtnormnlmenloptrnnetnnlsnumDerivopensslordinalpanpbkrtestpermutepillarpinfsc50pkgbuildpkgconfigpkgloadplot3DplotlyplotrixplyrpolynompraiseprettyunitsprincurveprocessxprogresspromisesproxypspurrrquadprogquantregR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenRcppParallelRcppProgressRCurlreadrrematch2reshape2rglrlangRLRsimrmarkdownrpartrprojrootrstatixrstudioapisassscalesshapesmacofspamSparseMstringistringrsurvivalsystestthattibbletidyrtidyselecttinytextzdbucminfutf8vcfRvctrsveganviridisviridisLitevroomwaldoweightswithrwordcloudxfunyamlzoo