Arguments
array.allocation
matrix with nArray rows and nRIL columns.
Elements of 1/0 indicate this RIL (or strain) is/not selected
for this array.
condition.allocation
matrix with nCondition rows and nRIL columns.
Elements of 1/0 indicate this RIL (or strain) is/not selected
for this condition.
nRILs
number of RILs (or strains) available for the experiment.
nSlides
total number of slides available for experiment.
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.
nTuple
average number of RILs (or strains) to be assigned onto each condition.
nTuple should be a real number which is larger than 1.
If nTuple < 1, the algorithm will stop and show the message,
warning: "The number of slides is too small to perform the experiment."
bTwoColorArray
binary variable indicating experiment type:
bTwoColorArray <- TRUE \#for dual channel experiment
bTwoColorArray <- FALSE \#for single channel experiment