pathfindR (version 1.3.0)

active_snw_search: Perform Active Subnetwork Search

Description

Perform Active Subnetwork Search

Usage

active_snw_search(input_for_search, pin_path, snws_file = "active_snws",
  dir_for_parallel_run = NULL, score_quan_thr = 0.8,
  sig_gene_thr = 10, search_method = "GR", silent_option = TRUE,
  use_all_positives = FALSE, geneInitProbs = 0.1, saTemp0 = 1,
  saTemp1 = 0.01, saIter = 10000, gaPop = 400, gaIter = 10000,
  gaThread = 5, gaMut = 0, grMaxDepth = 1, grSearchDepth = 1,
  grOverlap = 0.5, grSubNum = 1000)

Arguments

input_for_search

input the input data that active subnetwork search uses. The input must be a data frame containing at least these three columns:

describe

HGNC Gene Symbol

P_VALUE

p value obtained through a test, e.g. differential expression/methylation

pin_path

path to the Protein Interaction Network (PIN) file used in the analysis

snws_file

name for active subnetwork search output data

dir_for_parallel_run

directory for parallel run iteration. Only used in the wrapper function (see ?run_pathfindR) (Default = NULL)

score_quan_thr

active subnetwork score quantile threshold (Default = 0.80)

sig_gene_thr

threshold for minimum number of significant genes (Default = 10)

search_method

algorithm to use when performing active subnetwork search. Options are greedy search (GR), simulated annealing (SA) or genetic algorithm (GA) for the search (Default = GR).

silent_option

boolean value indicating whether to print the messages to the console (FALSE) or print to a file (TRUE) during active subnetwork search (default = TRUE). This option was added because during parallel runs, the console messages get mixed up.

use_all_positives

if TRUE: in GA, adds an individual with all positive nodes. In SA, initializes candidate solution with all positive nodes. (Default = FALSE)

geneInitProbs

For SA and GA, probability of adding a gene in initial solution (Default = 0.1)

saTemp0

Initial temperature for SA (Default = 1.0)

saTemp1

Final temperature for SA (Default = 0.01)

saIter

Iteration number for SA (Default = 10000)

gaPop

Population size for GA (Default = 400)

gaIter

Iteration number for GA (Default = 200)

gaThread

Number of threads to be used in GA (Default = 5)

gaMut

For GA, applies mutation with given mutation rate (Default = 0, i.e. mutation off)

grMaxDepth

Sets max depth in greedy search, 0 for no limit (Default = 1)

grSearchDepth

Search depth in greedy search (Default = 1)

grOverlap

Overlap threshold for results of greedy search (Default = 0.5)

grSubNum

Number of subnetworks to be presented in the results (Default = 1000)

Value

A list of genes in every identified active subnetwork that has a score greater than the `score_quan_thr`th quantile and that has at least `sig_gene_thr` affected genes.

Examples

# NOT RUN {
active_snw_search(input_for_search, pin_path = "path/to/PIN", search_method = "GR")
active_snw_search(input_for_search, pin_path = "path/to/PIN",
search_method = "SA", saTemp0 = 2, saTemp1 = 0.05)
# }