SAGA: Software for the Analysis of Genetic Architecture

Implements an information theory approach to the analysis of line cross data providing model averaged results of parameter estimates and unconditional standard errors. Also includes functions to provide a visualization of models space, custom plots of multi-model inference results, and traditional line cross analysis plots.

Author
Heath Blackmon and Jeffery P. Demuth
Date of publication
2015-12-03 13:05:04
Maintainer
Heath Blackmon <coleoguy@gmail.com>
License
GPL (>= 2)
Version
2.0.0
URLs

View on CRAN

Man pages

AICtoMW
converts AIC or AICc to model weights
AnalyzeCrossesMM
Multimodel Analysis of Line Cross Data
cohortID
Display a lookup table for cohort IDs
data
empirical datasets
DisplayCmatrix
Display a matrix of composite genetic effects
EvaluateModel
Evaluate Single Model
plot.genarch
provides a custom plot of a genarch object
plotObserved
provides the traditional line cross analysis plot.
SAGA-package
Software for the Analysis of Genetic Architecture SAGA
VisModelSpace
Visualize Model Space

Files in this package

SAGA
SAGA/inst
SAGA/inst/cmatrix.xy.csv
SAGA/inst/doc
SAGA/inst/doc/model-averaged-analysis.R
SAGA/inst/doc/model-averaged-analysis.pdf
SAGA/inst/doc/model-averaged-analysis.Rmd
SAGA/inst/cmatrix.zw.csv
SAGA/inst/genome.scale.csv
SAGA/inst/cmatrix.esd.csv
SAGA/NAMESPACE
SAGA/data
SAGA/data/SR.rda
SAGA/data/PH.rda
SAGA/data/ban.osa.rda
SAGA/data/dar.bho.rda
SAGA/data/per.inf.rda
SAGA/data/sin.cro.rda
SAGA/data/SL.rda
SAGA/R
SAGA/R/EvaluateModel.R
SAGA/R/plot.genarch.R
SAGA/R/VisModelSpace.R
SAGA/R/cohortID.R
SAGA/R/AnalyzeCrossesMM.R
SAGA/R/AICtoMW.R
SAGA/R/DisplayCmatrix.R
SAGA/R/plotObserved.R
SAGA/vignettes
SAGA/vignettes/model-averaged-analysis.Rmd
SAGA/MD5
SAGA/build
SAGA/build/vignette.rds
SAGA/DESCRIPTION
SAGA/man
SAGA/man/VisModelSpace.Rd
SAGA/man/AnalyzeCrossesMM.Rd
SAGA/man/cohortID.Rd
SAGA/man/plot.genarch.Rd
SAGA/man/DisplayCmatrix.Rd
SAGA/man/data.Rd
SAGA/man/EvaluateModel.Rd
SAGA/man/plotObserved.Rd
SAGA/man/AICtoMW.Rd
SAGA/man/SAGA-package.Rd