# Inference for predictive networks designed for (but not limited to) genomic data

## Documentation for package ‘predictionet’ version 1.2.2

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

predictionet-package | Inference for predictive networks designed for (but not limited to) genomic data
adj.descent | Function to identify all children of a parent
adj.remove.cycles | Function to remove cycles that may be present in a directed graph represented by an adjacency matrix
annot.ras | Gene expression, annotations, clinical data and priors for the colon cancer tumors collected by the expression project for oncology (expO).
annot2.ras | Gene expression, annotations, clinical data and priors for the colon cancer tumors collected by Jorissen and colleagues in 2009.
data.discretize | Function to discretize data based on user specified cutoffs
data.ras | Gene expression, annotations, clinical data and priors for the colon cancer tumors collected by the expression project for oncology (expO).
data2.ras | Gene expression, annotations, clinical data and priors for the colon cancer tumors collected by Jorissen and colleagues in 2009.
demo.ras | Gene expression, annotations, clinical data and priors for the colon cancer tumors collected by the expression project for oncology (expO).
demo2.ras | Gene expression, annotations, clinical data and priors for the colon cancer tumors collected by Jorissen and colleagues in 2009.
eval.network | Function computing the f1-score, comparing an inferred topology with a given topology
expO.colon.ras | Gene expression, annotations, clinical data and priors for the colon cancer tumors collected by the expression project for oncology (expO).
jorissen.colon.ras | Gene expression, annotations, clinical data and priors for the colon cancer tumors collected by Jorissen and colleagues in 2009.
mcc | Function to compute the Matthews Correlation Coefficient (MCC) in a classification framework
net.stab | Function evaluating the stability of a network inferred from data with a specific method
net2topo | Function transforming a network model into an adjacency matrix: parents in rows, children in columns
netinf | Function performing network inference by combining priors and genomic data
netinf.cv | Function performing network inference by combining priors and genomic data
netinf.predict | Function to make prediction of a node values given its parents using an inferred network
netinf2gml | Function to create an 'igraph' object and export a network to a GML readable by Cytoscape
pred.score | Function computing performance of prediction; methods include r2, nrmse and mcc
predictionet | Inference for predictive networks designed for (but not limited to) genomic data
priors.ras | Gene expression, annotations, clinical data and priors for the colon cancer tumors collected by the expression project for oncology (expO).
priors2.ras | Gene expression, annotations, clinical data and priors for the colon cancer tumors collected by Jorissen and colleagues in 2009.