COSINE: COndition SpecIfic sub-NEtwork
Version 2.1

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

AuthorHaisu Ma
Date of publication2014-07-10 07:34:03
MaintainerHaisu Ma <haisu.ma.pku.2008@gmail.com>
LicenseGPL (>= 2)
Version2.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("COSINE")

Getting started

Package overview

Popular man pages

cond.fyx: Compute the ECF-statistics measuring the differential...
COSINE-package: COndition SpecIfic subNEtwork identification
diff_gen: Calculate the F-statistics and ECF-statistics
GA_search_PPI: Run genetic algorithm to search for the PPI sub-network
get_quantiles: Get the five quantiles of the weight parameter lambda
PPI: The protein protein interaction network data
scaled_edge_score: The scaled ECF statistics of all the edges
See all...

All man pages Function index File listing

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

Functions

COSINE Man page
COSINE-package Man page
DataSimu Man page Source code
GA_search Man page Source code
GA_search_PPI Man page Source code
PPI Man page
Score_adjust_PPI Man page Source code
choose_lambda Man page Source code
cond.fyx Man page Source code
diff_gen Man page Source code
diff_gen_PPI Man page Source code
diff_gen_for3 Man page Source code
f.test Man page Source code
get_components_PPI Man page Source code
get_quantiles Man page Source code
get_quantiles_PPI Man page Source code
random_network_sampling_PPI Man page Source code
scaled_edge_score Man page
scaled_node_score Man page
score_scaling Man page Source code
set1_GA Man page
set1_scaled_diff Man page
set1_unscaled_diff Man page
simulated_data Man page

Files

NAMESPACE
data
data/PPI.rda
data/scaled_node_score.rda
data/set1_scaled_diff.rda
data/scaled_edge_score.rda
data/simulated_data.rda
data/datalist
data/set1_unscaled_diff.rda
data/set1_GA.rda
R
R/diff_gen_PPI.R
R/get_components_PPI.R
R/COSINE-internal.R
R/GA_search.R
R/f.test.R
R/score_scaling.R
R/DataSimu.R
R/get_quantiles.R
R/random_network_sampling_PPI.R
R/Score_adjust_PPI.R
R/GA_search_PPI.R
R/get_quantiles_PPI.R
R/cond.fyx.R
R/diff_gen_for3.R
R/diff_gen.R
R/choose_lambda.R
MD5
DESCRIPTION
man
man/random_network_sampling_PPI.Rd
man/GA_search_PPI.Rd
man/simulated_data.Rd
man/get_quantiles.Rd
man/GA_search.Rd
man/diff_gen.Rd
man/PPI.Rd
man/f.test.Rd
man/get_components_PPI.Rd
man/diff_gen_for3.Rd
man/score_scaling.Rd
man/diff_gen_PPI.Rd
man/COSINE-package.Rd
man/cond.fyx.Rd
man/DataSimu.Rd
man/get_quantiles_PPI.Rd
man/set1_scaled_diff.Rd
man/Score_adjust_PPI.Rd
man/scaled_node_score.Rd
man/scaled_edge_score.Rd
man/choose_lambda.Rd
man/set1_unscaled_diff.Rd
man/set1_GA.Rd
COSINE documentation built on May 19, 2017, 11:02 a.m.

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