diamond_db: diamond function wrapper

In ddeweerd/MODifieRDB: MODifieRDB

Description

diamond function wrapper

Usage

diamond_db(
  input_name,
  ppi_name,
  deg_cutoff = 0.05,
  to_db = TRUE,
  folder = NULL,
  n_output_genes = 200,
  seed_weight = 10,
  include_seed = F,
  module_name,
  con
)

Arguments

input_name	Name of the input object in the database
ppi_name	Name of the PPI network in the database
deg_cutoff	p-value cutoff for differentialy expressed genes
to_db	Save result in database, default is TRUE
folder	If not saved in database, folder where to save the module as .rds
n_output_genes	maximum number of genes to be included in the final module
seed_weight	Numeric additional parameter to assign weight for the seed genes
include_seed	Logical TRUE/FALSE for inclusion of seed genes in the output module
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 diamond method.

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