Infers biological signatures from gene expression data

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Documentation for package ‘Pigengene’ version 1.34.0

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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