eval.network


Inferred topology, an edge between to variables X and Y corresponds to net[X,Y]=1.

topo


topology the user wants to compare the inferred topology with, e.g. the true network using generated datasets. An edge between to variables X and Y corresponds to net[X,Y]=1.

true.topo


This function computes the f1-score for an inferred topology using a topology provided by the user.


 graphs

This package contains a set of functions related to
network inference combining genomic data and prior information
extracted from biomedical literature and structured biological
databases. The main function is able to generate networks using
Bayesian or regression-based inference methods; while the
former is limited to < 100 of variables, the latter may infer
networks with hundreds of variables. Several statistics at the
edge and node levels have been implemented (edge stability,
predictive ability of each node, ...) in order to help the user
to focus on high quality subnetworks. Ultimately, this package
is used in the 'Predictive Networks' web application developed
by the Dana-Farber Cancer Institute in collaboration with
Entagen.

Benjamin HaibeKains

predictionet

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