Package index • phyloDE

Phylogenetic Differential Expression

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

phyloDE-package phyloDE: The phyloDE Package for Differential Expression Analysis
phylolmFit(): Phylogenetic Linear Model for Gene Expression Analysis
phylogeneticCorrelations(): Phylogenetic Correlation using a Consensus Tree

S4 Classes

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

PhyloMArrayLM-class: Class PhyloMArrayLM
ConsensusTreeModel-class: Class ConsensusTreeModel
getParameters() plotParameters() show(<PhyloMArrayLM>) show(<ConsensusTreeModel>) logLikelihood() consensusTree(): Methods for classes PhyloMArrayLM and ConsensusTreeModel

Helper Functions

Function to pre-process the tree or the data.

phyHeatmap(): Heatmap with Phylogeny Structured Columns
addReplicatesOnTree(): Add replicates to a tree
lengthNormalizeRNASeq(): Normalize RNASeq count data using gene lengths
rhoFromAlpha() alphaFromRho(): Compute rho parameter
getBoundsSelectionStrength(): Get Bounds on alpha for an OU
getMinError(): Get Lower Bound on sigma2_error

Dataset

Crayfish dataset

crayfish: Crayfish RNA-Seq dataset