getDrugMatrix

Obtaining drug-disease reverse association score matrix.

A systematic biology tool was developed to prioritize cancer subtype-specific drugs by integrating genetic perturbation, drug action, biological pathway, and cancer subtype.
The capabilities of this tool include inferring patient-specific subpathway activity profiles in the context of gene expression profiles with subtype labels, calculating differentially
expressed subpathways based on cultured human cells treated with drugs in the 'cMap' (connectivity map) database, prioritizing cancer subtype specific drugs according to drug-disease
reverse association score based on subpathway, and visualization of results (Castelo (2013) <doi:10.1186/1471-2105-14-7>; Han et al (2019) <doi:10.1093/bioinformatics/btz894>; Lamb and Justin (2006) <doi:10.1126/science.1132939>). Please cite using <doi:10.1093/bioinformatics/btab011>.

Junwei Han

SubtypeDrug

Prioritization of Candidate Cancer Subtype Specific Drugs

getDrugMatrix function

<dl><dt>spw_matrix</dt>
<dd>A subpathway activity profile. rows are subpathwyas, columns are samples.</dd>
<dt>drug_target_data</dt>
<dd>A list. A list stores a collection of drug up- and down-regulated subpathways.</dd>
<dt>weighted.score</dt>
<dd>A binary value of 0 or 1. If the `weighted.score` = 1, the drug reverse association score will be weighted by the subpathway activity.</dd></dl>

Arguments

Xudong Han,
Junwei Han,
Chonghui Liu

Author

SubtypeDrug internal function — getDrugMatrix

<dl>

<dt>spw_matrix</dt>
<dd>A subpathway activity profile. rows are subpathwyas, columns are samples.</dd>


<dt>drug_target_data</dt>
<dd>A list. A list stores a collection of drug up- and down-regulated subpathways.</dd>


<dt>weighted.score</dt>
<dd>A binary value of 0 or 1. If the `weighted.score` = 1, the drug reverse association score will be weighted by the subpathway activity.</dd>

</dl>

getDrugMatrix: SubtypeDrug internal function

Description

Usage

Value

Arguments

Author

Details

Examples