COSINE (version 2.0)

COSINE-package: COndition SpecIfic subNEtwork identification

Description

This is a package to identify the single globally optimal subnetwork which differs the most between two or more datasets

Details

ll{ Package: COSINE Type: Package Version: 2.0 Date: 2014-03-25 License: GPL (version 2 or later) LazyLoad: yes } install.packages("COSINE")

Examples

set.seed(666)

simulated_data <- DataSimu()

set1_data<-simulated_data[[1]][,1:100]

control_data<-simulated_data[[7]][,1:100]

diff_set1 <- diff_gen(set1_data,control_data)

scaled_diff_set1 <- score_scaling(diff_expr=diff_set1[[1]],
diff_coex=diff_set1[[2]])

klist<-c(25,30)

set1_quantile<-get_quantiles(diff_expr=scaled_diff_set1[[1]],
diff_coex=scaled_diff_set1[[2]],klist,pop_size=10)

lambda<-set1_quantile[[2]]

set1_GA<-GA_search(lambda,diff_expr=scaled_diff_set1[[1]],
diff_coex=scaled_diff_set1[[2]], num_iter=1, muCh=0.05, zToR=10)

set1_choose_lambda <- choose_lambda(diff_expr=scaled_diff_set1[[1]],
diff_coex=scaled_diff_set1[[2]],lambda,
subnet_size=set1_GA$Subnet_size,num_random_sampling=10,
best_score=set1_GA$Best_Scores)