AnovaTest {MM4LMM} | R Documentation |
This function computes Type I and Type III tests for each fixed effect of a model, as displayed by the MMEst
function. Alternatively, a specific linear combination of the fixed parameters may be tested (at 0).
AnovaTest(ResMMEst , TestedCombination=NULL , Type = "TypeIII" , NbCores=1)
ResMMEst |
A list as displayed by the |
TestedCombination |
A contrast matrix or a list of contrast matrices C_m. Each matrix corresponds to a (set of) linear combination to be (jointly) tested at 0. |
Type |
Either "TypeI" of "TypeIII" (default is "TypeIII"). AnovaTest will compute tests of the given type for each fixed effect in the model. The option is ignored if a |
NbCores |
The number of cores to be used. |
If no TestedCombination
is provided, the function performs either Type I or Type III tests for each fixed effect in the model (default is Type III). If TestedCombination
is provided, each linear combination in TestedCombination
is tested at 0 using a Wald test. No check is performed regarding the estimability of the linear combination to be tested. If the dimension of the combination does not match with the dimension of ResMMEst
, a NA
is returned.
The output of the function is a list with as many items as in the original input list ResMMEst
. For each item of ResMMEst
, a table is provided that contains the Wald test statistics, p-values and degrees of freedom for all tested hypotheses.
F. Laporte and T. Mary-Huard
require('MM4LMM') data(QTLDetectionExample) Pheno <- QTLDetectionExample$Phenotype Geno <- QTLDetectionExample$Genotype Kinship <- QTLDetectionExample$Kinship ##Build the VarList object VL <- list(Additive = Kinship , Error = diag(1,length(Pheno))) ##Perform inference Result <- MMEst(Y=Pheno , X = Geno , VarList = VL) ##Compute tests AOV <- AnovaTest(Result,Type="TypeI") ##Test specific contrast matrix TC = matrix(c(0,1),nrow=1) AOV2 <- AnovaTest(Result, TestedCombination = TC)