adjustMixedDir

Adjusting the PDAG matrix to model constraints
This function can be used to adjust the adjacency matrix to model constraints, such as blacklist and background nodes

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

adjustMixedDir function

<dl><dt>adj</dt>
<dd>adjacency matrix representing a graph or posterior probabilities of all its edges</dd>
<dt>bnnames</dt>
<dd>object of class bnNames</dd>
<dt>blacklist</dt>
<dd>a square matrix with same dimensions as adj representing edges prohibited by the model</dd></dl>

Arguments

Adjusting the PDAG matrix to model constraints
This function can be used to adjust the adjacency matrix to model constraints, such as blacklist and background nodes — adjustMixedDir

<dl>

<dt>adj</dt>
<dd>adjacency matrix representing a graph or posterior probabilities of all its edges</dd>


<dt>bnnames</dt>
<dd>object of class bnNames</dd>


<dt>blacklist</dt>
<dd>a square matrix with same dimensions as adj representing edges prohibited by the model</dd>

</dl>

Adjusting the PDAG matrix to model constraints
This function can be used to adjust the adjacency matrix to model constraints, such as blacklist and background nodes

adjustMixedDir: Adjusting the PDAG matrix to model constraints This function can be used to adjust the adjacency matrix to model constraints, such as blacklist and background nodes

Description

Usage

Value

Arguments