ConAn

Differential Network Connectivity Analysis

Documentation

Please visit https://montilab.github.io/ConAn

Requirements

We recommend the latest version of R (>= 4.0.0) but ConAn currently requires R (>= 3.6.0) to be installed directly from Github.

Install with devtools

library(devtools)
devtools::install_github("montilab/ConAn")

library(ConAn)

Example

simulations <- readRDS(file.path(system.file("extdata", package="ConAn"), "simulations.rds"))

eset <- simulations$eset
pathways <- simulations$pathways
names(pathways) <- paste("P", seq(length(pathways)), sep="")

output <- conan(eset=eset,
                mod_list=pathways,
                covariate="group",
                ctrl="G1",
                cond="G2",
                sim_type=c("bootstrap", "permutation")[[1]],
                iter=20,
                mean_correct=TRUE,
                N_genes=1000,
                iter_bg=50,
                cores=1,
                mdc_type=c("fraction", "difference")[[2]],
                plotting=TRUE,
                FUN = c(cor, bicor)[[1]])