Entry: acceptanceProbability
Aliases: acceptanceProbability
Keywords: method
Description: Compute the acceptance probability for each updated design
URL: ../../../library/designGG/html/acceptanceProbability.html

Entry: arrayUpdate
Aliases: arrayUpdate
Keywords: method
Description: Update array allocation
URL: ../../../library/designGG/html/arrayUpdate.html

Entry: conditionAllocation
Aliases: conditionAllocation
Keywords: method
Description: Allocate the selected RILs into different conditions
URL: ../../../library/designGG/html/conditionAllocation.html

Entry: conditionCombination
Aliases: conditionCombination
Keywords: method
Description: Generate a matrix indicating all possible levels for environmental factors
URL: ../../../library/designGG/html/conditionCombination.html

Entry: conditionLevel
Aliases: conditionLevel
Keywords: method
Description: Levels of all environmental factors
URL: ../../../library/designGG/html/conditionLevel.html

Entry: conditionUpdate
Aliases: conditionUpdate
Keywords: method
Description: Update condition allocation
URL: ../../../library/designGG/html/conditionUpdate.html

Entry: designGG
Aliases: designGG design genetical genomics experiment
Keywords: method
Description: Optimal design for genetical genomics experiments
URL: ../../../library/designGG/html/designGG.html

Entry: designScore
Aliases: designScore
Keywords: method
Description: Calculate the A- or D- optimality score based on current experimental design
URL: ../../../library/designGG/html/designScore.html

Entry: exampleArrayDesignTable
Aliases: exampleArrayDesignTable
Keywords: datasets
Description: Example output of ArrayDesignTable data
URL: ../../../library/designGG/html/exampleArrayDesignTable.html

Entry: exampleConditionDesignTable
Aliases: exampleConditionDesignTable
Keywords: datasets
Description: Example ConditionDesignTable data
URL: ../../../library/designGG/html/exampleConditionDesignTable.html

Entry: examplePlotObj
Aliases: examplePlotObj
Keywords: datasets
Description: Example PlotObj data
URL: ../../../library/designGG/html/examplePlotObj.html

Entry: experimentDesignTable
Aliases: experimentDesignTable
Keywords: method
Description: Make experiment table based design matrix
URL: ../../../library/designGG/html/experimentDesignTable.html

Entry: genotype
Aliases: genotype
Keywords: datasets
Description: Example genotype data
URL: ../../../library/designGG/html/genotype.html

Entry: initialDesign
Aliases: initialDesign
Keywords: method
Description: Initialize an experiment design matrix
URL: ../../../library/designGG/html/initialDesign.html

Entry: interactionLevel
Aliases: interactionLevel
Keywords: method
Description: Generate levels for all interacting factors
URL: ../../../library/designGG/html/interactionLevel.html

Entry: pairLevel
Aliases: pairLevel
Keywords: method
Description: Pair levels for paired RILs (or strains)
URL: ../../../library/designGG/html/pairLevel.html

Entry: plotAllScores
Aliases: plotAllScores
Keywords: method
Description: Plot scores profiles
URL: ../../../library/designGG/html/plotAllScores.html

Entry: temperatureStep
Aliases: temperatureStep
Keywords: 
Description: Calculate the temperature decreasing step for simulated annealing process
URL: ../../../library/designGG/html/temperatureStep.html

Entry: updateDesign
Aliases: updateDesign
Keywords: method
Description: Updates current design
URL: ../../../library/designGG/html/updateDesign.html

Entry: variableNames
Aliases: variableNames
Keywords: method
Description: Generate variable names for all factors
URL: ../../../library/designGG/html/variableNames.html

Entry: variableNumber
Aliases: variableNumber
Keywords: method
Description: Compute the number of variables in the experiment
URL: ../../../library/designGG/html/variableNumber.html
