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COSINE (version 2.0)

COndition SpecIfic sub-NEtwork

Description

To identify the globally most discriminative subnetwork from gene expression profiles using an optimization model and genetic algorithm

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Version

Install

install.packages('COSINE')

Monthly Downloads

19

Version

2.0

License

GPL (>= 2)

Maintainer

Haisu Ma

Last Published

March 27th, 2014

Functions in COSINE (2.0)

GA_search

Use genetic algorithm to search for the globally optimal subnetwork
diff_gen

Calculate the F-statistics and ECF-statistics
simulated_data

The simulated data sets used in the paper
set1_scaled_diff

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

Get the five quantiles of the weight parameter lambda
f.test

To get the F-statistics for each gene
COSINE-package

COndition SpecIfic subNEtwork identification
DataSimu

Simulation of the six datasets and the case dataset
set1_unscaled_diff

The unstandardized F-statistics and ECF-statistics of simulated dataset 1
set1_GA

Result of genetic algorithm search for simulated data set1
cond.fyx

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

To get the normalzied F-statistics and ECF-statistics