|
This package provides functions for the integrated analysis of biological networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values derived from statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of genes from an Affymetrix array are assigned to the nodes of an protein-protein interaction network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.
● Data Source:
BioConductor
● Keywords:
● Alias: BioNet, BioNet-package
●
0 images
|
The function aggregates several p-values into one p-value of p-values based on the order statistics of p-values. An overall p-value is given by the ith order statistic.
● Data Source:
BioConductor
● Keywords:
● Alias: aggrPvals
●
3 images
|
|
The function fits a beta-uniform mixture model to a given p-value distribution.
● Data Source:
BioConductor
● Keywords:
● Alias: bumOptim
●
0 images
|
The function compares the following parameters of two networks: diameter, average degree, degree exponent, average path length and plots the cumulative degree distributions. The networks have to be connected components.
● Data Source:
BioConductor
● Keywords:
● Alias: compareNetworks
●
1 images
|
|
The function calculates consensus scores for a network, given a list of replicate modules.
● Data Source:
BioConductor
● Keywords:
● Alias: consensusScores
●
0 images
|
fbum
(Package: BioNet) :
Compute the density of the bum distribution
Function to compute the density of the beta-uniform mixture model.
● Data Source:
BioConductor
● Keywords:
● Alias: fbum
●
0 images
|
|
The function calculates the log likelihood of the BUM model.
● Data Source:
BioConductor
● Keywords:
● Alias: fbumLL
●
0 images
|
|
The function calculates the p-value threshold tau for a given false discovery rate. Tau is used for the scoring function.
● Data Source:
BioConductor
● Keywords:
● Alias: fdrThreshold
●
0 images
|
The function fits a beta-uniform mixture model to a given p-value distribution. The BUM method was introduced by Stan Pounds and Steve Morris to model the p-value distribution as a signal-noise decompostion. The signal component is assumed to be B(a,1)-distributed, whereas the noise component is uniform-distributed under the null hypothesis.
● Data Source:
BioConductor
● Keywords:
● Alias: fitBumModel
●
1 images
|
getCompScores
(Package: BioNet) :
Partition scores for subgraphs of the network
The function partitions the scores into scores for each subgraph of the network.
● Data Source:
BioConductor
● Keywords:
● Alias: getCompScores
●
0 images
|
providing 
.