conditionLevel {designGG}R Documentation

Levels of all environmental factors


Describe the levels of all environmental factors for each RIL/strain in the experiment.
This is a subfunction needed for designScore, but is not directly used.


    conditionLevel( array.allocation, condition.allocation, 
                    condition.combination,nEnvFactors )



a matrix with nArray rows and nRIL columns. Elements of 1/0 indicates this RIL (or strain) is/not selected for this array.


a matrix with nCondition rows and nRIL columns. Elements of 1/0 indicates this RIL (or strain) is/not selected for this condition.


a matrix indicating all possible levels for environmental factors, with dimension of nConditions by nEnvFactors.


number of environmental factors, an integer bewteen 1 and 3. When nEnvFactors is 1 and nLevels is 1, there is one condition in the experiment (i.e. no enviromental perturbation) and thus only genetic factor will be considered in the algorithm. When nEnvFactors is 1 and nLevels is larger than 1 or nEnvFactors is larger than 1, all main factor(s) and interacting facotr(s) will be included.


For single-channel experiment, array.allocation is NULL. Then the conditionLevel is decided by condition.allocation. For dual-channel experiment, array.allocation decides which RILs are selected and then the condition.allocation indicates which condition this RIL will be put in for the experiment.


A matrix with dimension of nRILs by nEnvFactors, each element indicates the level of a certain environmental factor to which the RIL (or strain) is exposed in the experiment.


Yang Li <>, Gonzalo Vera <>
Rainer Breitling <>, Ritsert Jansen <>


Y. Li, R. Breitling and R.C. Jansen. Generalizing genetical genomics: the added value from environmental perturbation, Trends Genet (2008) 24:518-524.
Y. Li, M. Swertz, G. Vera, J. Fu, R. Breitling, and R.C. Jansen. designGG: An R-package and Web tool for the optimal design of genetical genomics experiments. BMC Bioinformatics 10:188(2009)

See Also

designScore, conditionCombination

[Package designGG version 1.1 Index]