Description Usage Arguments Details Value Author(s) References See Also
Generate levels for all interacting factors for all RILs (or strains).
This is a subfunction needed for designScore
, but is not directly used.
1 2 | interactionLevel( genotype.level, condition.level, markerIndex,
nEnvFactors )
|
genotype.level |
levels of genetic factor for each RIL (or strain) in the experiment. |
condition.level |
levels of all environmental factors for each RIL (or strain)in the experiment. |
markerIndex |
indicate which genome position that level of genetic factor corresponds to. |
nEnvFactors |
number of environmental factors, an integer bewteen 1 and 3.
When |
markerIndex
indicates the genome position that genotype.level
corresponds
to.
An experiment design is defined to be optimal over all markers if
the sum of scores, e.g. A-optimality criterion over all markers is
minimized.
a matrix with nRILs rows. The number columns depends on nEnvFactors
.
For example:
If nEnvFactors
= 1, there is only one interaction term.
If nEnvFactors
= 2, there are three pair-wise two-way interaction terms and one
three-way interaction term.
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
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