LinearSystemMatrix

Returns a matrix from output of <code>PenalisedLinearSystem</code>.

In stability selection (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>) and consensus clustering (S Monti et al (2003) <doi:10.1023/A:1023949509487>), resampling techniques are used to enhance the reliability of the results. In this package, hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2023a) <doi:10.1093/jrsssc/qlad058> and B Bodinier et al (2023b) <doi:10.1093/bioinformatics/btad635>). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.

Barbara Bodinier

sharp

Stability-enHanced Approaches using Resampling Procedures

LinearSystemMatrix function

<dl><dt>vect</dt>
<dd>vector of coefficients to assign to entries of the matrix.</dd>
<dt>adjacency</dt>
<dd>binary adjacency matrix of the Directed Acyclic Graph
(transpose of the asymmetric matrix A in Reticular Action Model notation).
The row and column names of this matrix must be defined.</dd></dl>

Arguments

Matrix from linear system outputs — LinearSystemMatrix

<dl>

<dt>vect</dt>
<dd>vector of coefficients to assign to entries of the matrix.</dd>


<dt>adjacency</dt>
<dd>binary adjacency matrix of the Directed Acyclic Graph
(transpose of the asymmetric matrix A in Reticular Action Model notation).
The row and column names of this matrix must be defined.</dd>

</dl>

LinearSystemMatrix: Matrix from linear system outputs

Description

Usage

Value

Arguments

See Also