Class PhyloMArrayLM

Extension of class MArrayLM-class from package limma for phylogenetically correlated regressions of gene-wise linear models.

It is a simple list-based S4 class. Objects are normally created by phylolmFit. Additional components are added by eBayes.

Components

PhyloMArrayLM objects do not contain any slots (apart from .Data) but they should contain the same list components than MArrayLM-class.

In addition, they contain the following tree-specific components:

phy:

The phylogenetic tree used for the regression, of class phylo.

modelphy:

The phylogenetic model of trait evolution, argument call in phylolmFit.

measurement_error:

Boolean, TRUE if there is additional measurement error, argument call in phylolmFit.

phy_trans:

List of the transformed phylogenetic trees obtained from a fit using phylolm on each gene.

optpar:

Vector of the optpar obtained from a fit using phylolm on each gene.

lambda_error:

Vector of the lambda_error parameters obtained from a fit using phylolm on each gene.

sigma2_phy:

Vector of the phylogenetic sigma2 parameters obtained from a fit using phylolm on each gene.

sigma2_error:

Vector of the sigma2_error parameters obtained from a fit using phylolm on each gene.

See also

MArrayLM-class, phylolmFit.