single_iter_wrapper {pathfindR}

Active Subnetwork Search + Enrichment Analysis Wrapper for a Single Iteration

Description

Active Subnetwork Search + Enrichment Analysis Wrapper for a Single Iteration

Usage

single_iter_wrapper(
  i = NULL,
  dirs,
  input_processed,
  pin_path,
  score_quan_thr,
  sig_gene_thr,
  search_method,
  silent_option,
  use_all_positives,
  geneInitProbs,
  saTemp0,
  saTemp1,
  saIter,
  gaPop,
  gaIter,
  gaThread,
  gaCrossover,
  gaMut,
  grMaxDepth,
  grSearchDepth,
  grOverlap,
  grSubNum,
  gset_list,
  adj_method,
  enrichment_threshold,
  list_active_snw_genes
)

Arguments

i

current iteration index (default = NULL)

dirs

vector of directories for parallel runs

input_processed

processed input data frame

pin_path

path/to/PIN/file

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

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 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.

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)

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)

gset_list

list for gene sets

adj_method

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

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)

Value

Data frame of enrichment results using active subnetwork search results