penUpdateInter

This function can be used to update an existing penalization matrix

Unsupervised Bayesian network-based clustering of multi-omics data. Both binary and continuous data types
are allowed as inputs. The package serves a dual purpose: it clusters (patient) samples and learns the multi-omics networks that characterize discovered
clusters. Prior network knowledge (e.g., public interaction databases) can be included via blacklisting and
penalization matrices. For clustering, the EM algorithm is employed. For structure search at the M-step,
the Bayesian approach is used. The output includes membership assignments of samples, cluster-specific MAP networks, and posterior probabilities
of all edges in the discovered networks. In addition to likelihood, AIC and BIC scores are returned. They can be used for choosing the number
of clusters.
References:
P. Suter et al. (2021) <doi:10.1101/2021.12.16.473083>,
J. Kuipers and P. Suter and G. Moffa (2022) <doi:10.1080/10618600.2021.2020127>,
J. Kuipers et al. (2018) <doi:10.1038/s41467-018-06867-x>.

Polina Suter

bnClustOmics

Bayesian Network-Based Clustering of Multi-Omics Data

Jack Kuipers

penUpdateInter function

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

Arguments

Author

Updating penalization matrix (between two omics types) — penUpdateInter

<dl>

<dt>penmat</dt>
<dd>a square penalization matrix; to initialize use penInit</dd>


<dt>bnnames</dt>
<dd>object of class bnInfo; see bnInfo</dd>


<dt>type1</dt>
<dd>name of omics type (from)</dd>


<dt>type2</dt>
<dd>name of omics type (to)</dd>


<dt>intlist</dt>
<dd>(optional) a matrix or data frame containing a list of interactions and optionally their scores; 2 columns are necessary 'gene1' and 'gene2'</dd>


<dt>pfbase</dt>
<dd>a numeric value more or equal to 1, base penalization factor; 2 by default (1 corresponds to no penalization)</dd>


<dt>intpf</dt>
<dd>(optional) a numeric value more or equal to 1, this value will be used to penalize interactions from 'intlist'</dd>


<dt>intsame</dt>
<dd>penalization factor for edges connecting the same genes</dd>


<dt>bi</dt>
<dd>(logical) indicates if interactions should be considered bi-directed</dd>

</dl>

penUpdateInter: Updating penalization matrix (between two omics types)

Description

Usage

Value

Arguments

Author