run_clustering: Module Detection
In mrbakhsh/HPiP: Host-Pathogen Interaction Prediction

run_clustering

R Documentation

Module Detection

Description

This function contains five module detection algorithms including fast-greedy algorithm (FC), walktrap algorithm (RW), multi-level community algorithm (ML), label propagation algorithm (clp), and markov clustering (MCL).

Usage

run_clustering(
  ppi,
  method = c("FC", "RW", "ML", "clp", "MCL"),
  expan = 2,
  infla = 5,
  iter = 50
)

Arguments

`ppi`	A data.frame containing pathogen proteins in the first column,host proteins in the second column, and edge weight in the third column.
`method`	Module detection algorithms including: `FC` - fast-greedy algorithm. `RW` - walktrap algorithm. `ML` - multi-level community algorithm. `clp` - label propagation algorithm. `MCL` - markov clustering.
`expan`	Numeric value > 1 for the expansion parameter. See `mcl` for more details.
`infla`	Numeric value > 0 for the inflation power coefficient. See `mcl` for more details.
`iter`	An integer, the maximum number of iterations for the MCL. See `mcl` for more details.