mcode_db: MCODE function wrapper

In ddeweerd/MODifieRDB: MODifieRDB

Description

MCODE function wrapper

Usage

mcode_db(
  input_name,
  ppi_name,
  to_db = TRUE,
  folder = NULL,
  hierarchy = 1,
  vwp = 0.5,
  haircut = F,
  fluff = F,
  fdt = 0.8,
  loops = T,
  deg_cutoff = 0.05,
  module_cutoff = 3.5,
  module_name,
  con
)

Arguments

input_name	Name of the input object in the database
ppi_name	Name of the PPI network in the database
to_db	Save result in database, default is TRUE
folder	If not saved in database, folder where to save the module as .rds
hierarchy	This parameter indicates how many hierarchy are included in the network, currently it can be 0, 1 or 2. Default value is 1.
vwp	Vertex weight percentage. Default value is 0.5.
haircut	Boolean value, whether to remove singly-connected nodes from clusters (TRUE) or not (FALSE).
fluff	Boolean value, whether to spand cluster cores by one neighbour shell outwards (TRUE) or not (FALSE).
fdt	Cluster density cutoff. Default value is 0.8.
loops	Boolean value, whether to include self-loops (TRUE) or not (FALSE).
deg_cutoff	p-value cutoff for differentialy expressed genes
module_cutoff	Minimal score for a module to be returned
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 mcode method.

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