designGG: Computational tool for designing genetical genomics experiments.

The package provides R scripts for designing genetical genomics experiments.

Author
Yang Li <yang.li@rug.nl>, Morris Swertz <m.a.swertz@rug.nl>, Gonzalo Vera <gonzalo.vera.rodriguez@gmail.com>, Rainer Breitling <r.breitling@rug.nl>, Ritsert Jansen <r.c.jansen@rug.nl>
Date of publication
2013-02-19 16:08:27
Maintainer
Yang Li <yang.li@rug.nl>
License
GPL
Version
1.1
URLs

View on CRAN

Man pages

acceptanceProbability
Compute the acceptance probability for each updated design
arrayUpdate
Update array allocation
conditionAllocation
Allocate the selected RILs into different conditions
conditionCombination
Generate a matrix indicating all possible levels for...
conditionLevel
Levels of all environmental factors
conditionUpdate
Update condition allocation
designGG
Optimal design for genetical genomics experiments
designScore
Calculate the A- or D- optimality score based on current...
exampleArrayDesignTable
Example output of ArrayDesignTable data
exampleConditionDesignTable
Example ConditionDesignTable data
examplePlotObj
Example PlotObj data
experimentDesignTable
Make experiment table based design matrix
genotype
Example genotype data
initialDesign
Initialize an experiment design matrix
interactionLevel
Generate levels for all interacting factors
pairLevel
Pair levels for paired RILs (or strains)
plotAllScores
Plot scores profiles
temperatureStep
Calculate the temperature decreasing step for simulated...
updateDesign
Updates current design
variableNames
Generate variable names for all factors
variableNumber
Compute the number of variables in the experiment

Files in this package

designGG
designGG/MD5
designGG/R
designGG/R/variableNumber.R
designGG/R/variableNames.R
designGG/R/updateDesign.R
designGG/R/temperatureStep.R
designGG/R/plotAllScores.R
designGG/R/pairLevel.R
designGG/R/nSlidesANDnTuple.R
designGG/R/interactionLevel.R
designGG/R/initialDesign.R
designGG/R/experimentDesignTable.R
designGG/R/designScore.R
designGG/R/designGG.R
designGG/R/conditionUpdate.R
designGG/R/conditionLevel.R
designGG/R/conditionCombination.R
designGG/R/conditionAllocation.R
designGG/R/arrayUpdate.R
designGG/R/acceptanceProbability.R
designGG/NAMESPACE
designGG/man
designGG/man/variableNumber.Rd
designGG/man/variableNames.Rd
designGG/man/updateDesign.Rd
designGG/man/temperatureStep.Rd
designGG/man/plotAllScores.Rd
designGG/man/pairLevel.Rd
designGG/man/interactionLevel.Rd
designGG/man/initialDesign.Rd
designGG/man/genotype.Rd
designGG/man/experimentDesignTable.Rd
designGG/man/examplePlotObj.Rd
designGG/man/exampleConditionDesignTable.Rd
designGG/man/exampleArrayDesignTable.Rd
designGG/man/designScore.Rd
designGG/man/designGG.Rd
designGG/man/designGG-internal.rd
designGG/man/conditionUpdate.Rd
designGG/man/conditionLevel.Rd
designGG/man/conditionCombination.Rd
designGG/man/conditionAllocation.Rd
designGG/man/arrayUpdate.Rd
designGG/man/acceptanceProbability.Rd
designGG/DESCRIPTION
designGG/data
designGG/data/genotype.rda
designGG/data/examplePlotObj.rda
designGG/data/exampleConditionDesignTable.rda
designGG/data/exampleArrayDesignTable.rda