| variableNames {designGG} | R Documentation |
Generate variable names for genetic, environmental factors and interacting terms.
variableNames(nEnvFactors)
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.
|
generates names for variables, a vector with the length of (variableNumber+1).
When nEnvFactors = 1 and nLevels = 1, there is no environmetal pertubation in the experimental.
Then we re-define nEnvFactors to be 0 within the algorithm. Accordingly, variableNumber = 1, and
variableNames is one genetic factor "Q".
When nEnvFactors = 1, variableNumber = 3, and
variableNames are one genetic factor "Q", one environmental factor "F",
and one interacting factor "QxF".
When nEnvFactors = 2, variableNumber = 7, and variableNames are one genetic factor "Q",
two environmental factors "F1" and "F2",
three two-way interacting factors "QF1", "QF2", "F1F2",
and one three way interacting factors "QxF1xF2".
When nEnvFactors = 3, variableNumber = 15, and
variableNames are one genetic factor "Q",
three environmental factors "F1", "F2" and "F3",
six two-way interacting factors "QF1", "QF2", "QF3", "F1F2",
"F2F3" and "F1F3",
four three-way interacting factors "QxF1xF2", "QxF1xF3",
"QxF2xF3", "F1xF2xF3"
and one four-way interacting factors "QxF1xF2xF3".
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. (submitted)
http://gbic.biol.rug.nl/designGG