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. |