process_drug_target_interactions

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

process_drug_target_interactions function

<dl><dt>drug_target_interactions</dt>
<dd>data frame containing drugs and target genes</dd>
<dt>PIN_genes</dt>
<dd>gene symbols for the chosen PIN</dd>
<dt>drug_name_col</dt>
<dd>name of the column containing drug names (default = "drug_name")</dd>
<dt>target_col</dt>
<dd>name of the column containing drug targets (default = "converted_target_gene")</dd></dl>

Arguments

Process Drug-Target Interactions — process_drug_target_interactions

<dl>

<dt>drug_target_interactions</dt>
<dd>data frame containing drugs and target genes</dd>


<dt>PIN_genes</dt>
<dd>gene symbols for the chosen PIN</dd>


<dt>drug_name_col</dt>
<dd>name of the column containing drug names (default = "drug_name")</dd>


<dt>target_col</dt>
<dd>name of the column containing drug targets (default = "converted_target_gene")</dd>

</dl>

process_drug_target_interactions: Process Drug-Target Interactions

Description

Usage

Value

Arguments