Wrapper for Active Subnetwork Search + Enrichment over Single/Multiple Iteration(s)

Wrapper for Active Subnetwork Search + Enrichment over Single/Multiple Iteration(s)

active_snw_enrichment_wrapper(
  input_processed,
  pin_path,
  gset_list,
  enrichment_threshold,
  list_active_snw_genes,
  adj_method = "bonferroni",
  search_method = "GR",
  disable_parallel = FALSE,
  use_all_positives = FALSE,
  iterations = 10,
  n_processes = NULL,
  score_quan_thr = 0.8,
  sig_gene_thr = 0.02,
  saTemp0 = 1,
  saTemp1 = 0.01,
  saIter = 10000,
  gaPop = 400,
  gaIter = 200,
  gaThread = 5,
  gaCrossover = 1,
  gaMut = 0,
  grMaxDepth = 1,
  grSearchDepth = 1,
  grOverlap = 0.5,
  grSubNum = 1000,
  silent_option = TRUE
)

Arguments

input_processed

processed input data frame

pin_path

path/to/PIN/file

gset_list

list for gene sets

enrichment_threshold

adjusted-p value threshold used when filtering enrichment results (default = 0.05)

list_active_snw_genes

boolean value indicating whether or not to report the non-significant active subnetwork genes for the active subnetwork which was enriched for the given term with the lowest p value (default = FALSE)

adj_method

correction method to be used for adjusting p-values. (default = 'bonferroni')

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').

disable_parallel

boolean to indicate whether to disable parallel runs via foreach (default = FALSE)

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)

iterations

number of iterations for active subnetwork search and enrichment analyses (Default = 10)

n_processes

optional argument for specifying the number of processes used by foreach. If not specified, the function determines this automatically (Default == NULL. Gets set to 1 for Genetic Algorithm)

score_quan_thr

active subnetwork score quantile threshold. Must be between 0 and 1 or set to -1 for not filtering. (Default = 0.8)

sig_gene_thr

threshold for the minimum proportion of significant genes in the subnetwork (Default = 0.02) If the number of genes to use as threshold is calculated to be < 2 (e.g. 50 signif. genes x 0.01 = 0.5), the threshold number is set to 2

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)

gaCrossover

Applies crossover with the given probability in GA (default = 1, i.e. always perform crossover)

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)

silent_option

boolean value indicating whether to print the messages to the console (FALSE) or not (TRUE, this will print to a temp. file) during active subnetwork search (default = TRUE). This option was added because during parallel runs, the console messages get disorderly printed.

Value

Data frame of combined pathfindR enrichment results