Integrate omic datasets using PCSF — kinograte • kinograte

This function integrates omic datasets using prize-collecting Steiner forest (PCSF) algorithm

Usage

kinograte(
  df,
  ppi_network,
  n = 10,
  w = 10,
  r = 0.1,
  b = 2,
  mu = 0.005,
  cluster = TRUE,
  seed = NULL
)

df: combined ranked omic datasets
ppi_network: dataframe of protein-protein interactions
n: An integer value to determine the number of runs with random noise added edge costs. A default value is 10.
w: A numeric value for tuning the number of trees in the output. A default value is 2.
r: A numeric value to determine additional random noise to edge costs. A random noise upto r percent of the edge cost is added to each edge. A default value is 0.1
b: A numeric value for tuning the node prizes. A default value is 1.
mu: A numeric value for a hub penalization. A default value is 0.0005.
cluster: set TRUE to cluster the network
seed: (optional) set seed number

list(network, nodes, edges)