Initialize an experiment design matrix
Allocate RILs (or strains) into different conditional and pair RILs (or strains) into slides.
genotype data: a nMarker-by-nRILs matrix with two allels being 0 and 1 (or A and B) or three allels being 0, 0.5 and 1 (or, A, H, and B), where 0.5 (or H) represents heterozygous allele.
total number of RILs ((or strains) available for the experiment.
total number of slides available for the experiment.
number of all possible combination of all environmental factors.
average number of RILs (or strains) to be assigned onto each condition
binary variable indicating experiment type:
For two-color array experiments, randomly choose a RIL (or strain) and pair it with the
genetically most different RIL (or strain) on one array.
For one-color array experiments, array.allocation is
NULL as there is no
need to pair samples.
a list with 2 matrices:
condition.allocation: allocate RILs (or strains) into different conditional
(nCondition * nRILs)
array.allocation: pair RILs (or strains) into sldies
(nSlides * nRILs)
This function calls
conditionAllocation function to allocate selected RILs
(or strains) into different conditions.
Yang Li <email@example.com>, Gonzalo Vera <firstname.lastname@example.org>
Rainer Breitling <email@example.com>, Ritsert Jansen <firstname.lastname@example.org>
Y. Li, R. Breitling and R.C. Jansen. Generalizing genetical
genomics: the added value from environmental perturbation, Trends Genet
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)
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