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COSINE (version 1.0)

COndition SpecIfic sub-NEtwork

Description

To identify the globally most discriminative subnetwork from gene expression profiles and protein-protein interactions data using an optimization method and genetic algorithm

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Version

Install

install.packages('COSINE')

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Version

1.0

License

GPL (>= 2)

Maintainer

Haisu Ma

Last Published

July 23rd, 2012

Functions in COSINE (1.0)

COSINE-package

COndition SpecIfic subNEtwork identification

scaled_edge_score

The scaled ECF statistics of all the edges

PPI

The protein protein interaction network data

get_quantiles

Get the five quantiles of the weight parameter lambda

diff_gen

Calculate the F-statistics and ECF-statistics

random_network_sampling_PPI

To sample random sub-network from the PPI data

diff_gen_PPI

Generate the scaled node score and scaled edge score for nodes and edges in the background network

choose_lambda

Choose the most appropriate weight parameter lambda

diff_gen_for3

Generate the F-statistics and ECF-statistics for the comparison of three datasets

get_quantiles_PPI

Get the five quantile values of lambda for analysis of gene expression and PPI network data

scaled_node_score

The scaled ECF-statistics of all the edges

set1_GA

Result of genetic algorithm search for simulated data set1

score_scaling

To get the normalzied F-statistics and ECF-statistics

get_components_PPI

Get all the components (connected clusters) of the sub-network

simulated_data

The simulated data sets used in the paper

GA_search_PPI

Run genetic algorithm to search for the PPI sub-network

DataSimu

Simulation of the six datasets and the case dataset

set1_unscaled_diff

The unstandardized F-statistics and ECF-statistics of simulated dataset 1

cond.fyx

Compute the ECF-statistics measuring the differential correlation of gene pairs

GA_search

Use genetic algorithm to search for the globally optimal subnetwork

f.test

To get the F-statistics for each gene

Score_adjust_PPI

To adjust the score of the selected PPI sub-network using random sampling

set1_scaled_diff

The standardized F-statistics and ECF-statistics for the comparison between simulated data1 and the control data