8. Clique filtering

Clique filtering is a technique used to remove “random-like” networks when working with binary similarity and very sparse data. Data types include copy number variations, which are few per patient.

Motivation section TBA

8.1. Output format of cliqueFilterNets.R

A data.frame with per-network stats on clique-filtering:

  • NETWORK: network name
  • orig_pp: Num (+,+) interactions.
  • orig_rest: Num (+,-) and (-,-) interactions
  • ENR: Enrichment or bias of (+,+) interactions relative to other interactions. Specifically defined as (orig_pp-orig_rest)/(orig_pp+orig_rest). Ranges between -1 (all non-(+,+)) to +1 (all (+,+)).
  • TOTAL_INT: orig_pp+orig_rest
  • numPerm: num permutations done in clique filtering
  • shuf_mu: mean ENR of permuted nets (i.e. mean null ENR)
  • shuf_sigma: standard deviation of ENR of permuted nets (i.e. s.d. of null ENR)
  • Z: Z-score of ENR in real network, relative to null distribution
  • pctl: Percentile of ENR in real network, relative to null distribution. Also the p-value
  • Q: Benjamini-Hochberg corrected pvalue.