kinograte: Integrate omic datasets using PCSF

In kalganem/Kinograte: Kinograte: Netwrok-based multi-omics Integration

Integrate omic datasets using PCSF

Description

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
)

Arguments

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

Value

list(network, nodes, edges)

kalganem/Kinograte documentation built on April 27, 2022, 9:03 p.m.