lmem.qtler: Linear Mixed Effects Models for QTL Mapping for Multienvironment and Multitrait Analysis

Performs QTL mapping analysis for balanced and for multi-environment and multi-trait analysis using mixed models. Balanced population, single trait, single environment QTL mapping is performed through marker-regression (Haley and Knott (1992) <DOI:10.1038/hdy.1992.131>, Martinez and Curnow (1992) <DOI:10.1007/BF00222330>, while multi-environment and multi-trait QTL mapping is performed through linear mixed models. These functions could use any of the following populations: double haploid, F2, recombinant inbred lines, back-cross, and 4-way crosses. Performs a Single Marker Analysis, a Single Interval Mapping, or a Composite Interval Mapping analysis, and then constructs a final model with all of the relevant QTL.

Author
Lucia Gutierrez [aut], Gaston Quero [aut, cre], Schubert Fernandez [aut], Sofia Brandariz [aut], Sebastian Simondi [ctb]
Date of publication
2016-07-12 07:49:42
Maintainer
Gaston Quero <gastonquero@gmail.com>
License
GPL-3
Version
0.1.1

View on CRAN

Man pages

DHpop_geno
Name of the file containing genotypic (marker scores)...
DHpop_map
Name of the file containing genotypic (marker scores)...
DHpop_pheno
Name of the file containing genotypic (marker scores)...
mq.diagnostics
Performs molecular markers quality diagnostics.
pq.diagnostics
Performs phenotypic data quality diagnostics.
qtl.analysis
Performs a balanced population QTL mapping analysis.
qtl.cross
Read genomic data to perform QTL analyses.
qtl.memq
Performs Multi-Environment (or Multi-Trait) Multi-QTL...
SxM_geno
Name of the file containing genotypic (marker scores)...
SxM_map
Name of the file containing genotypic (marker scores)...
SxM_pheno
Name of the file containing phenotypic information.
SxMxE_pheno
Name of the file containing phenotypic information.

Files in this package

lmem.qtler
lmem.qtler/inst
lmem.qtler/inst/CITATION
lmem.qtler/inst/doc
lmem.qtler/inst/doc/lmem.qtler.Rmd
lmem.qtler/inst/doc/lmem.qtler.html
lmem.qtler/inst/doc/lmem.qtler.R
lmem.qtler/NAMESPACE
lmem.qtler/data
lmem.qtler/data/SxMxE_pheno.rda
lmem.qtler/data/DHpop_pheno.rda
lmem.qtler/data/SxM_pheno.rda
lmem.qtler/data/DHpop_geno.rda
lmem.qtler/data/SxM_map.rda
lmem.qtler/data/SxM_geno.rda
lmem.qtler/data/DHpop_map.rda
lmem.qtler/R
lmem.qtler/R/DHpop_pheno.R
lmem.qtler/R/SxM_map.R
lmem.qtler/R/diagnosis_functions.R
lmem.qtler/R/qtl.cross.R
lmem.qtler/R/SxM_geno.R
lmem.qtler/R/DHpop_geno.R
lmem.qtler/R/qtl.analysis.R
lmem.qtler/R/DHpop_map.R
lmem.qtler/R/SxM_pheno.R
lmem.qtler/R/SxMxE_pheno.R
lmem.qtler/R/qtl.memq.R
lmem.qtler/vignettes
lmem.qtler/vignettes/lmem.qtler.Rmd
lmem.qtler/MD5
lmem.qtler/build
lmem.qtler/build/vignette.rds
lmem.qtler/DESCRIPTION
lmem.qtler/man
lmem.qtler/man/DHpop_pheno.Rd
lmem.qtler/man/qtl.cross.Rd
lmem.qtler/man/SxM_geno.Rd
lmem.qtler/man/DHpop_geno.Rd
lmem.qtler/man/SxM_map.Rd
lmem.qtler/man/pq.diagnostics.Rd
lmem.qtler/man/qtl.analysis.Rd
lmem.qtler/man/SxMxE_pheno.Rd
lmem.qtler/man/SxM_pheno.Rd
lmem.qtler/man/DHpop_map.Rd
lmem.qtler/man/mq.diagnostics.Rd
lmem.qtler/man/qtl.memq.Rd