network_propagation

Network Propagation (Random-walk with Restart)

Identification of the most appropriate pharmacotherapy for each
patient based on genomic alterations is a major challenge in personalized
oncology. 'PANACEA' is a collection of personalized anti-cancer drug
prioritization approaches utilizing network methods. The methods utilize
personalized "driverness" scores from 'driveR' to rank drugs, mapping these
onto a protein-protein interaction network. The "distance-based" method
scores each drug based on these scores and distances between drugs and genes
to rank given drugs. The "RWR" method propagates these scores via a
random-walk with restart framework to rank the drugs. The methods are
described in detail in Ulgen E, Ozisik O, Sezerman OU. 2023. PANACEA:
network-based methods for pharmacotherapy prioritization in personalized
oncology. Bioinformatics <doi:10.1093/bioinformatics/btad022>.

Ege Ulgen

PANACEA

Personalized Network-Based Anti-Cancer Therapy Evaluation

network_propagation function

<dl><dt>prior_vec</dt>
<dd>vector of prior knowledge on selected genes (names are gene symbols)</dd>
<dt>W_prime</dt>
<dd>(Laplacian-normalized, symmetric) adjacency matrix</dd>
<dt>alpha</dt>
<dd>restart parameter, controlling trade-off between prior information and network smoothing</dd>
<dt>max.iter</dt>
<dd>maximum allowed number of iterations (default = 1000)</dd>
<dt>eps</dt>
<dd>epsilon value to assess the L2 norm of the difference between iterations (default = 1e-4)</dd></dl>

Arguments

Network Propagation (Random-walk with Restart) — network_propagation

<dl>

<dt>prior_vec</dt>
<dd>vector of prior knowledge on selected genes (names are gene symbols)</dd>


<dt>W_prime</dt>
<dd>(Laplacian-normalized, symmetric) adjacency matrix</dd>


<dt>alpha</dt>
<dd>restart parameter, controlling trade-off between prior information and network smoothing</dd>


<dt>max.iter</dt>
<dd>maximum allowed number of iterations (default = 1000)</dd>


<dt>eps</dt>
<dd>epsilon value to assess the L2 norm of the difference between iterations (default = 1e-4)</dd>

</dl>

network_propagation: Network Propagation (Random-walk with Restart)

Description

Usage

Value

Arguments

Details