# Infers biological signatures from gene expression data

## Documentation for package ‘Pigengene’ version 1.35.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

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 | Infers robust biological signatures from gene expression data
pigengene | An object of class 'Pigengene'
pigengene-class | The pigengene class
plot-method | 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