MCL_tuning

This function optimize the choice of MCL algorithm
parameter (inflation) by comparing clustering-derived partitions for each
paramter values to known labels (i.e., CORUM complexes) and
assess the similarity between them using quality measures including
overlap score, sensitivity (Sn),
clustering-wise positive predictive value (PPV), geometric accuracy (Acc),
and maximum matching raio (MMR). It is recommended to first reduce
redundancy in the known reference complexes
via <code>EliminateCpxRedundance</code>, then performs parameter tuning.

The MACP employs machine learning algorithm for automated scoring
of co-fractionation mass spectrometry (CF-MS) and then systematically
map multi-protein complexes from these high-confidence protein-protein
interactions (PPIs) using unsupervised learning (i.e., clustering).

Matineh Rahmatbakhsh

MACP

Macromolecular Assemblies from Co-Elution Profile (MACP)

Mohan Babu

MCL_tuning function

<dl><dt>hc_ppi</dt>
<dd>Interactions data containing id1-id2-weight triplets.</dd>
<dt>predcpx</dt>
<dd>A data.frame containing predicted modules resulted from
<code>get_clusters</code>.</dd>
<dt>refcpx</dt>
<dd>A list containing reference complexes
(i.e., corum complexes).</dd>
<dt>inflation</dt>
<dd>A vector of integer, representing
MCL inflation parameter</dd>
<dt>csize</dt>
<dd>An integer, the minimum size of the predicted complexes.
Defaults to 2.</dd></dl>

Arguments

Matineh Rahmatbakhsh, <a href="/link/matinerb.94%40gmail.com?package=MACP&version=0.1.0" data-mini-rdoc="MACP::matinerb.94@gmail.com">matinerb.94@gmail.com</a>

Author

MCL Hyperparameters Tuning — MCL_tuning

<dl>

<dt>hc_ppi</dt>
<dd>Interactions data containing id1-id2-weight triplets.</dd>


<dt>predcpx</dt>
<dd>A data.frame containing predicted modules resulted from
<code>get_clusters</code>.</dd>


<dt>refcpx</dt>
<dd>A list containing reference complexes
(i.e., corum complexes).</dd>


<dt>inflation</dt>
<dd>A vector of integer, representing
MCL inflation parameter</dd>


<dt>csize</dt>
<dd>An integer, the minimum size of the predicted complexes.
Defaults to 2.</dd>

</dl>

Matineh Rahmatbakhsh, <a href='mailto:matinerb.94@gmail.com'>matinerb.94@gmail.com</a>

MCL_tuning: MCL Hyperparameters Tuning

Description

Usage

Value

Arguments

Author

Details