penUpdateInter: Updating penalization matrix (between two omics types)

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

Updating penalization matrix (between two omics types)

Description

This function can be used to update an existing penalization matrix

Usage

penUpdateInter(
  penmat,
  bnnames,
  type1,
  type2,
  intlist = NULL,
  pfbase = 2,
  intpf = 1,
  intsame = 1,
  bi = FALSE
)

Arguments

penmat	a square penalization matrix; to initialize use penInit
bnnames	object of class bnInfo; see bnInfo
type1	name of omics type (from)
type2	name of omics type (to)
intlist	(optional) a matrix or data frame containing a list of interactions and optionally their scores; 2 columns are necessary 'gene1' and 'gene2'
pfbase	a numeric value more or equal to 1, base penalization factor; 2 by default (1 corresponds to no penalization)
intpf	(optional) a numeric value more or equal to 1, this value will be used to penalize interactions from 'intlist'
intsame	penalization factor for edges connecting the same genes
bi	(logical) indicates if interactions should be considered bi-directed

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.