Package: qtlpoly 0.2.4

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://gabrielgesteira.r-universe.dev', 'https://cloud.r-project.org'))

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:

polyploid qtl-mapping

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

Last updated 6 days agofrom:96e99f0300. Checks:OK: 9. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 14 2024
R-4.5-win-x86_64	OK	Nov 14 2024
R-4.5-linux-x86_64	OK	Nov 14 2024
R-4.4-win-x86_64	OK	Nov 14 2024
R-4.4-mac-x86_64	OK	Nov 14 2024
R-4.4-mac-aarch64	OK	Nov 14 2024
R-4.3-win-x86_64	OK	Nov 14 2024
R-4.3-mac-x86_64	OK	Nov 14 2024
R-4.3-mac-aarch64	OK	Nov 14 2024

Exports:breeding_values feim fit_model fit_model2 modify_qtl null_model null_model2 optimize_qtl permutations plot_profile plot_qtl plot_sint profile_qtl qtl_effects read_data read_data2 remim remim2 search_qtl simulate_qtl

Dependencies:abind ape askpass backports base64enc bit bit64 bitops boot broom bslib cachem car carData checkmate class cli clipr cluster codetools colorspace CompQuadForm corrplot cowplot cpp11 crayon crosstalk curl data.table dendextend Deriv digest doBy doParallel dotCall64 dplyr e1071 ellipse evaluate fansi farver fastmap fields fontawesome forcats foreach foreign Formula fs gdata generics ggplot2 ggpubr ggrepel ggsci ggsignif glmnet glue gridExtra gtable gtools haven highr Hmisc hms htmlTable htmltools htmlwidgets httr isoband iterators jomo jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lme4 magrittr mappoly maps MASS Matrix MatrixModels memoise memuse mgcv mice microbenchmark mime minqa misc3d mitml modelr munsell mvtnorm nlme nloptr nnet nnls numDeriv openssl ordinal pan pbkrtest permute pillar pinfsc50 pkgconfig plot3D plotly plotrix plyr polynom prettyunits princurve progress promises proxy purrr quadprog quantreg R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen RcppParallel RcppProgress RCurl readr reshape2 rlang RLRsim rmarkdown rpart rstatix rstudioapi sass scales shape smacof spam SparseM stringi stringr survival sys tibble tidyr tidyselect tinytex tzdb ucminf utf8 vcfR vctrs vegan viridis viridisLite vroom weights withr wordcloud xfun yaml zoo

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Autotetraploid potato dataset	B2721
Prediction of QTL-based breeding values from REMIM model	breeding_values plot.qtlpoly.bvalues
Fixed-effect interval mapping (FEIM)	feim print.qtlpoly.feim
Fits multiple QTL models	fit_model summary.qtlpoly.fitted
Fits multiple QTL models	fit_model2
Simulated autohexaploid dataset.	hexafake
Autotetraploid potato map	maps4x
Simulated autohexaploid map	maps6x
Modify QTL model	modify_qtl print.qtlpoly.modify
Null model	null_model print.qtlpoly.null
Null model	null_model2
Model optimization	optimize_qtl print.qtlpoly.optimize
Fixed-effect interval mapping (FEIM) model permutations	permutations plot.qtlpoly.perm print.qtlpoly.perm
Autotetraploid potato phenotypes	pheno4x
Simulated phenotypes	pheno6x
Logarithm of _P_-value (LOP) profile plots	plot_profile
QTL heritability and significance plot	plot_qtl
QTLs with respective support interval plots	plot_sint
QTL profiling	print.qtlpoly.profile profile_qtl
QTL allele effect estimation	plot.qtlpoly.effects qtl_effects
Read genotypic and phenotypic data	print.qtlpoly.data read_data
Read genotypic and phenotypic data	read_data2
Random-effect multiple interval mapping (REMIM)	print.qtlpoly.remim remim
Random-effect multiple interval mapping (REMIM)	remim2
QTL forward search	print.qtlpoly.search search_qtl
Simulations of multiple QTL	print.qtlpoly.simul simulate_qtl