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


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Documentation for package ‘predictionet’ version 1.2.2

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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.