correlation_clique_db: correlation_clique function wrapper

In ddeweerd/MODifieRDB: MODifieRDB

Description

correlation_clique function wrapper

Usage

correlation_clique_db(
  input_name,
  ppi_name,
  frequency_cutoff = 0.5,
  to_db = TRUE,
  folder = NULL,
  fraction_of_interactions = 0.4,
  iteration = 50,
  clique_significance = 0.01,
  deg_cutoff = 0.05,
  multiple_cores = FALSE,
  n_cores = 3,
  module_name,
  con
)

Arguments

input_name	Name of the input object in the database
ppi_name	Name of the PPI network in the database
frequency_cutoff	Fraction of the number of times a gene should be present in it iterations. Default is 0.5, meaning 50 procent of all iterations
to_db	Save result in database, default is TRUE
folder	If not saved in database, folder where to save the module as .rds
fraction_of_interactions	Fraction of interactions from the original network that will be used in each iteration
iteration	Number of iterations to be performed
clique_significance	Cutoff for Fisher exact test for cliques
deg_cutoff	p-value cutoff for differentialy expressed genes
multiple_cores	parallelize iterations using number of cores on system -1?
n_cores	Number of cores to use
module_name	Unique name for the module object when stored in database
con	Database connection obtained with connect_to_db function

Details

Retrieves a MODifieR input object from database by input_name and runs correlation_clique method.

ddeweerd/MODifieRDB documentation built on Feb. 5, 2021, 1:50 a.m.