COSINE: COndition SpecIfic sub-NEtwork

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

Author
Haisu Ma
Date of publication
2014-07-10 07:34:03
Maintainer
Haisu Ma <haisu.ma.pku.2008@gmail.com>
License
GPL (>= 2)
Version
2.1

View on CRAN

Man pages

choose_lambda
Choose the most appropriate weight parameter lambda
cond.fyx
Compute the ECF-statistics measuring the differential...
COSINE-package
COndition SpecIfic subNEtwork identification
DataSimu
Simulation of the six datasets and the case dataset
diff_gen
Calculate the F-statistics and ECF-statistics
diff_gen_for3
Generate the F-statistics and ECF-statistics for the...
diff_gen_PPI
Generate the scaled node score and scaled edge score for...
f.test
To get the F-statistics for each gene
GA_search
Use genetic algorithm to search for the globally optimal...
GA_search_PPI
Run genetic algorithm to search for the PPI sub-network
get_components_PPI
Get all the components (connected clusters) of the...
get_quantiles
Get the five quantiles of the weight parameter lambda
get_quantiles_PPI
Get the five quantile values of lambda for analysis of gene...
PPI
The protein protein interaction network data
random_network_sampling_PPI
To sample random sub-network from the PPI data
scaled_edge_score
The scaled ECF statistics of all the edges
scaled_node_score
The scaled ECF-statistics of all the edges
Score_adjust_PPI
To adjust the score of the selected PPI sub-network using...
score_scaling
To get the normalzied F-statistics and ECF-statistics
set1_GA
Result of genetic algorithm search for simulated data set1
set1_scaled_diff
The standardized F-statistics and ECF-statistics for the...
set1_unscaled_diff
The unstandardized F-statistics and ECF-statistics of...
simulated_data
The simulated data sets used in the paper

Files in this package

COSINE
COSINE/NAMESPACE
COSINE/data
COSINE/data/PPI.rda
COSINE/data/scaled_node_score.rda
COSINE/data/set1_scaled_diff.rda
COSINE/data/scaled_edge_score.rda
COSINE/data/simulated_data.rda
COSINE/data/datalist
COSINE/data/set1_unscaled_diff.rda
COSINE/data/set1_GA.rda
COSINE/R
COSINE/R/diff_gen_PPI.R
COSINE/R/get_components_PPI.R
COSINE/R/COSINE-internal.R
COSINE/R/GA_search.R
COSINE/R/f.test.R
COSINE/R/score_scaling.R
COSINE/R/DataSimu.R
COSINE/R/get_quantiles.R
COSINE/R/random_network_sampling_PPI.R
COSINE/R/Score_adjust_PPI.R
COSINE/R/GA_search_PPI.R
COSINE/R/get_quantiles_PPI.R
COSINE/R/cond.fyx.R
COSINE/R/diff_gen_for3.R
COSINE/R/diff_gen.R
COSINE/R/choose_lambda.R
COSINE/MD5
COSINE/DESCRIPTION
COSINE/man
COSINE/man/random_network_sampling_PPI.Rd
COSINE/man/GA_search_PPI.Rd
COSINE/man/simulated_data.Rd
COSINE/man/get_quantiles.Rd
COSINE/man/GA_search.Rd
COSINE/man/diff_gen.Rd
COSINE/man/PPI.Rd
COSINE/man/f.test.Rd
COSINE/man/get_components_PPI.Rd
COSINE/man/diff_gen_for3.Rd
COSINE/man/score_scaling.Rd
COSINE/man/diff_gen_PPI.Rd
COSINE/man/COSINE-package.Rd
COSINE/man/cond.fyx.Rd
COSINE/man/DataSimu.Rd
COSINE/man/get_quantiles_PPI.Rd
COSINE/man/set1_scaled_diff.Rd
COSINE/man/Score_adjust_PPI.Rd
COSINE/man/scaled_node_score.Rd
COSINE/man/scaled_edge_score.Rd
COSINE/man/choose_lambda.Rd
COSINE/man/set1_unscaled_diff.Rd
COSINE/man/set1_GA.Rd