blInit

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

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

blInit function

<dl><dt>bnnames</dt>
<dd>object of class bnInfo; see bnInfo</dd>
<dt>bldiag</dt>
<dd>logical, defines if diagonal should be blacklisted, TRUE by default</dd>
<dt>intra</dt>
<dd>(optional) a vector of characters defining omic types for which intra-type edges will be blacklisted</dd>
<dt>interXX</dt>
<dd>(optional) a list containing two vectors of characters defining omic types between which same gene (X.type.from -&gt; X.type.to) edges will be blacklisted</dd>
<dt>interXY</dt>
<dd>(optional) a list containing two vectors of characters defining omic types between which different gene edges (X.type.from -&gt; Y.type.to) will be blacklisted</dd></dl>

Arguments

Author

Initializing blacklist — blInit

<dl>

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


<dt>bldiag</dt>
<dd>logical, defines if diagonal should be blacklisted, TRUE by default</dd>


<dt>intra</dt>
<dd>(optional) a vector of characters defining omic types for which intra-type edges will be blacklisted</dd>


<dt>interXX</dt>
<dd>(optional) a list containing two vectors of characters defining omic types between which same gene (X.type.from -&gt; X.type.to) edges will be blacklisted</dd>


<dt>interXY</dt>
<dd>(optional) a list containing two vectors of characters defining omic types between which different gene edges (X.type.from -&gt; Y.type.to) will be blacklisted</dd>

</dl>

blInit: Initializing blacklist

Description

Usage

Value

Arguments

Author