penInit: Initializing penalization matrix

In bnClustOmics: Bayesian Network-Based Clustering of Multi-Omics Data

Initializing penalization matrix

Description

This function can be used to initialize a penalization matrix for bnclustOmics clustering

Usage

penInit(
  bnnames,
  pfbase = 1,
  intpf = pfbase,
  intlist = NULL,
  intsame = 1,
  usescore = FALSE
)

Arguments

bnnames	object of class bnInfo; see bnInfo
pfbase	a numeric value more or equal to 1, base penalization factor; 1 by default (no penalization)
intpf	(optional) a numeric value more or equal to 1, this value will be used to penalize interactions from 'intlist'
intlist	(optional) a matrix or data frame containing a list of interactions and optionally their scores; 2 columns are necessary 'gene1' and 'gene2'
intsame	penalization factor for edges connecting the same genes
usescore	(logical) when TRUE, interactions score from column 'score' of the parameter 'intlist' will be used to define penalization factor

Value

returns a square matrix containing edge specific penalization factors

Author(s)

Polina Suter

bnClustOmics documentation built on Aug. 5, 2022, 5:11 p.m.