Pigengene-package       Infers robust biological signatures from gene
                        expression data
aml                     AML gene expression profile
apply.filter            Applies a given filter on the data
balance                 Balances the number of samples
calculate.beta          Estimates an appropriate power value
check.nas               Removes 'NA's from a data matrix
check.pigengene.input   Quality check on the imput
combine.networks        Combines two or more networks
compact.tree            Reduces the number of genes in a decision tree
compute.pigengene       Computes the eigengenes
dcor.matrix             Computes distance correlation for give matrix
determine.modules       Identifies modules of the network
draw.bn                 Draws a Bayesian network
eigengenes33            Eigengenes of 33 modules
gene.mapping            Maps gene IDs
get.enriched.pw         Performs pathway over representation analysis
get.fitted.leaf         Returs the leaf for each sample
get.genes               List the (most relevant) genes for a decision
                        tree.
get.used.features       Return the features used in a tree
learn.bn                Learns a Bayesian network
make.decision.tree      Creates a decision tree to classify samples
                        using the eigengenes values
make.filter             Computes the filter based on a similarity
                        network
mds                     MDS gene expression profile
message.if              Conditional messaging.
module.heatmap          Plots heatmaps for modules
one.step.pigengene      Runs the entire Pigengene pipeline
pheatmap.type           Plots heatmap with clustering only within
                        types.
pigengene               An object of class 'Pigengene'
pigengene-class         The pigengene class
plot.pigengene          Plots and saves a 'pigengene' object
preds.at                Prediction using a possibly compacted tree
project.eigen           Infers eigengenes for given expression data
pvalues.manova          Computes pvalues for multi-class differential
                        expression
save.if                 Saves an object verbosely.
wgcna.one.step          Module identification
