Package index • phyloDE

Phylogenetic Differential Expression

Functions to test for differential expression using moderated phylogenetic linear regression.

phyloDE-package phyloDE: TODO
phylolmFit(): Phylogenetic Comparative Method using LIMMA
phylogeneticCorrelations(): Phylogenetic correlation using a consensus tree

PhyloMArrayLM Class

Class containing the result of a fit and associated helper functions.

PhyloMArrayLM-class .PhyloMArrayLM: Class PhyloMArrayLM
consensus_tree(): Consensus tree of a `PhyloMArrayLM` object
eBayes() treat(): Empirical Bayes Statistics for Differential Expression
log_likelihood(): Log likelihood of a `PhyloMArrayLM` object
decideTests() classifyTestsF(): Multiple Testing Across Genes and Contrasts

Helper Functions

Function to pre-process the tree or the data.

addReplicatesOnTree(): Add replicates to a tree
lengthNormalizeRNASeq(): Normalize RNASeq count data using gene lengths