conan: Differential Connectivity

In montilab/ConAn: Differential Network Connectivity Analysis

Differential Connectivity

Description

Calculates the differential connectivity between two groups of samples across one or more modules of genes.

Usage

conan(
  eset,
  mod_list,
  covariate,
  ctrl,
  cond,
  sim_type = c("bootstrap", "permutation"),
  iter = 5,
  mean_correct = FALSE,
  N_genes = NULL,
  iter_bg = 1,
  cores = 1,
  mdc_type = c("difference", "fraction"),
  plotting = FALSE,
  FUN = cor,
  ...
)

Arguments

eset	An expression set object
mod_list	A list of character vectors
covariate	A string corresponding to column in pData distinguishing sample groups
ctrl	A string defining control samples
cond	A string defining condition samples
sim_type	Simulation type can be either c("bootstrap", "permutation")
iter	Number of sampling iterations during significance testing
mean_correct	Correct with background connectivity
N_genes	Number of randomly selected genes to be used during each iteration
iter_bg	Number of iterations used when calculating background (only used for non-NULL N_genes values
cores	Number of cores available for parallelization
mdc_type	Method for calculating difference in connectivity can be either c("fraction", "difference")
FUN	Function for calculating correlation

Value

A list of statistics and plots resulting from the analysis

montilab/ConAn documentation built on July 11, 2022, 6:42 p.m.