Other packages > Find by keyword >

mppR  

Multi-Parent Population QTL Analysis
View on CRAN: Click here


Download and install mppR package within the R console
Install from CRAN:
install.packages("mppR")

Install from Github:
library("remotes")
install_github("cran/mppR")

Install by package version:
library("remotes")
install_version("mppR", "1.5.0")



Attach the package and use:
library("mppR")
Maintained by
Vincent Garin
[Scholar Profile | Author Map]
First Published: 2018-07-01
Latest Update: 2023-01-05
Description:
Analysis of experimental multi-parent populations to detect regions of the genome (called quantitative trait loci, QTLs) influencing phenotypic traits measured in unique and multiple environments. The population must be composed of crosses between a set of at least three parents (e.g. factorial design, 'diallel', or nested association mapping). The functions cover data processing, QTL detection, and results visualization. The implemented methodology is described in Garin, Wimmer, Mezmouk, Malosetti and van Eeuwijk (2017) , in Garin, Malosetti and van Eeuwijk (2020) , and in Garin, Diallo, Tekete, Thera, ..., and Rami (2024) .
How to cite:
Vincent Garin (2018). mppR: Multi-Parent Population QTL Analysis. R package version 1.5.0, https://cran.r-project.org/web/packages/mppR. Accessed 29 Apr. 2025.
Previous versions and publish date:
1.1.10 (2018-07-01 15:30), 1.2.0 (2019-05-31 17:50), 1.2.1 (2020-02-11 22:10), 1.3.0 (2021-05-15 14:20), 1.4.0 (2023-01-05 21:50)
Other packages that cited mppR R package
View mppR citation profile
Other R packages that mppR depends, imports, suggests or enhances
Complete documentation for mppR
Functions, R codes and Examples using the mppR R package
Some associated functions: CV_partition . IBD.mppData . IBS.mppData . MQE_gen_effects . MQE_proc . QC.mppData . QTL_R2 . QTL_R2_GE . QTL_effect_GE . QTL_effect_QxEC . QTL_effect_main_QxE . QTL_forward . QTL_gen_effects . QTL_pred_R2 . QTL_select . USNAM_geno . USNAM_map . USNAM_pheno . create.mppData . design_connectivity . inc_mat_QTL . mppData . mppData_GE . mppData_add_pheno . mppData_init . mppData_mdf_pheno . mppGE_CIM . mppGE_SIM . mppGE_proc . mpp_CIM . mpp_CV . mpp_SIM . mpp_back_elim . mpp_forward . mpp_perm . mpp_proc . par_clu . parent_cluster.mppData . plot.QTLprof . plot_QTLxEC . plot_allele_eff_GE . print.summary.QR2Res . print.summary.QeffRes . print.summary.mppData . subset.mppData . summary.QR2Res . summary.QeffRes . summary.mppData . 
Some associated R codes: CV_partition.R . IBD.mppData.R . IBS.mppData.R . IncMat_QTL_MAF.R . IncMat_cross.R . IncMat_parent.R . IncMat_sum0_const.R . MM_QTL.R . MM_comp.R . MQE_BackElim.R . MQE_CIM.R . MQE_CIM_clu.R . MQE_R2.R . MQE_forward.R . MQE_genEffects.R . MQE_plot.R . MQE_proc.R . QC.mppData.R . QC_GenotypingError.R . QC_MAF.R . QC_hetero.R . QC_matchMarker.R . QC_minCrSize.R . QC_missing.R . QC_tagMAFCr.R . QTLModelBack.R . QTLModelCIM.R . QTLModelCIM_MQE.R . QTLModelPerm.R . QTLModelQeff.R . QTLModelSIM.R . QTL_CI.R . QTL_R2.R . QTL_R2_GE.R . QTL_effect_GE.R . QTL_effect_QxEC.R . QTL_effect_main_QxE.R . QTL_forward.R . QTL_gen_effects.R . QTL_pred_R2.R . QTL_pval.R . QTL_pval_mix.R . QTL_report.R . QTL_report_GE.R . QTL_select.R . Qeff_res_processing.R . Qeff_res_processing_MQE.R . Qprof_process.R . R2_lin.R . R2_lin_GE.R . R2_pred.R . W_QTL.R . W_test_Qpar_GxE.R . W_test_Qpar_main.R . check.MQE.R . check.cr.ABH.R . check.inf.R . check.model.comp.R . check.mpp.cv.R . check.mpp.proc.R . check_IBD.R . check_IBS.R . check_QC2.R . check_format_class.R . check_mod_mppGE.R . check_ref_par.R . cof_mat_reduce.R . color.code.R . create.mppData.R . cross_ABH.R . cross_ABH_het.R . design_connectectivity.R . determine_Qmain_QxE_sign.R . form_QTLxEC_mat.R . formula_backward.R . geno_012.R . getVCOV.R . inc_mat_QTL.R . lme_comp.R . mdf_par_name.R . mppData_add_pheno.R . mppData_mdf_pheno.R . mppGE_CIM.R . mppGE_SIM.R . mppGE_proc.R . mpp_CIM.R . mpp_CIM_clu.R . mpp_CV.R . mpp_SIM.R . mpp_SIM_clu.R . mpp_back_elim.R . mpp_forward.R . mpp_perm.R . mpp_proc.R . parent_cluster.mppData.R . parent_clusterCheck.R . plot.QTLprof.R . plot_CV.R . plot_QTLxEC.R . plot_allele_eff_GE.R . print.summary.QR2Res.R . print.summary.QeffRes.R . print.summary.mppData.R . reference.count.R . remove_singularities.R . sign.star.R . subset.mppData.R . summary.QR2Res.R . summary.QeffRes.R . summary.mppData.R .  Full mppR package functions and examples
Downloads during the last 30 days
03/3003/3104/0104/0204/0304/0404/0504/0604/0704/0804/0904/1004/1104/1204/1304/1404/1504/1604/1704/1804/1904/2004/2104/2204/2304/2404/2504/2604/2704/28Downloads for mppR0246810121416182022TrendBars

Today's Hot Picks in Authors and Packages

PCAmatchR  
Match Cases to Controls Based on Genotype Principal Components
Matches cases to controls based on genotype principal components (PC). In order to produce better r ...
Download / Learn more Package Citations See dependency  
quickcode  
Quick and Essential 'R' Tricks for Better Scripts
The NOT functions, 'R' tricks and a compilation of some simple quick plus often used 'R' codes to im ...
Download / Learn more Package Citations See dependency  
phecodemap  
Visualization for PheCode Mapping with ICD-9 and ICD-10-CM Codes
To build a shiny app for visualization of the hierarchy of PheCode Mapping with International Classi ...
Download / Learn more Package Citations See dependency  
bigGP  
Distributed Gaussian Process Calculations
Distributes Gaussian process calculations across nodes in a distributed memory setting, using Rmpi. ...
Download / Learn more Package Citations See dependency  
NBBDesigns  
Neighbour Balanced Block Designs (NBBDesigns)
Neighbour-balanced designs ensure that no treatment is disadvantaged unfairly by its surroundings. T ...
Download / Learn more Package Citations See dependency  
knockoff  
The Knockoff Filter for Controlled Variable Selection
The knockoff filter is a general procedure for controlling the false discovery rate (FDR) when perf ...
Download / Learn more Package Citations See dependency  

24,142

R Packages

207,311

Dependencies

65,176

Author Associations

24,143

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA