conditionLevel: Levels of all environmental factors

Description

Describe the levels of all environmental factors for each RIL/strain in the experiment. This is a subfunction needed for designScore, but is not directly used.

Usage

conditionLevel( array.allocation, condition.allocation,  condition.combination,nEnvFactors )

Arguments

array.allocation

a matrix with nArray rows and nRIL columns. Elements of 1/0 indicates this RIL (or strain) is/not selected for this array.

condition.allocation

a matrix with nCondition rows and nRIL columns. Elements of 1/0 indicates this RIL (or strain) is/not selected for this condition.

condition.combination

a matrix indicating all possible levels for environmental factors, with dimension of nConditions by nEnvFactors.

nEnvFactors

number of environmental factors, an integer bewteen 1 and 3. When nEnvFactors is 1 and 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.

Value

A matrix with dimension of nRILs by nEnvFactors, each element indicates the level of a certain environmental factor to which the RIL (or strain) is exposed in the experiment.

Details

For single-channel experiment, array.allocation is NULL. Then the conditionLevel is decided by condition.allocation. For dual-channel experiment, array.allocation decides which RILs are selected and then the condition.allocation indicates which condition this RIL will be put in for the experiment.

References