conditionCombination: Generate a matrix indicating all possible levels for...
In designGG: Computational tool for designing genetical genomics experiments.

Description Usage Arguments Details Value Author(s) References See Also

Generate a matrix indicating all possible levels for environmental factors with dimension nConditions * nEnvFactors. This is a subfunction needed for designScore, but is not directly used.

1	conditionCombination( nEnvFactors, nLevels, Level, envFactorNames )

`nEnvFactors`	number of environmental factors, an integer bewteen 1 and 3. When `nEnvFactors` is 1 and the number of levels for the enviromental factor (`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. Examples: If there is a temperature perturbation, then `nEnvFactors` is 1; If there is both temperature and drug treatment perturbation, then `nEnvFactors` is 2.
`nLevels`	number of levels for each factor, a vector with each component being integer. The length should be equal to `nEnvFactors`.
`Level`	a list which specifies the levels for each factor in the experiment. There are in total `nEnvFactors` elements in the list and each element correspsonds to certain envrironmental factor. The element is a vector describing all levels of the environmental factor. Default setting for the level of each factor is 1, 2, ...., nLevels[i]. (Here nLevels[i] is the ith element of nLevels, which tells the total number of levels for i environmental factor).
`envFactorNames`	a vector with names for all environmental factor(s). For example, for an experiment with two environmental factors of temperature and drug treatment: `envFactorNames <- c( "Temperature", "Dosage" )` Default = `NULL`, then the output will use `"F1"` and `"F2"` to indicate the environmental factors.

Currently this function works only when nEnvFactors is between 1 and 3.

A matrix with dimension of nConditions * nEnvFactors. Each element in the matrix indicates the levels of corresponding environmental factor.

Yang Li <yang.li@rug.nl>, Gonzalo Vera <gonzalo.vera.rodriguez@gmail.com>
Rainer Breitling <r.breitling@rug.nl>, Ritsert Jansen <r.c.jansen@rug.nl>

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)
http://gbic.biol.rug.nl/designGG

designScore

designGG documentation built on May 2, 2019, 5:51 a.m.