genesetCytoSig

Returns the gene set associated with input cytokine(s) from the CytoSig database
given manually specified cytokine-specific output csv file(s) under
the extdata directory with file name beginning with
the specified cytokine (i.e., 'IL6_output.csv') as currently provided for the IL6 cytokine.

Generates cell-level cytokine activity estimates using relevant information from gene sets constructed with the 'CytoSig' and the 'Reactome' databases and scored using the modified 'Variance-adjusted Mahalanobis (VAM)' framework for single-cell RNA-sequencing (scRNA-seq) data. 'CytoSig' database is described in: Jiang at al., (2021) <doi:10.1038/s41592-021-01274-5>. 'Reactome' database is described in: Gillespie et al., (2021) <doi:10.1093/nar/gkab1028>. The 'VAM' method is outlined in: Frost (2020) <doi:10.1093/nar/gkaa582>.

Azka Javaid

scaper

Single Cell Transcriptomics-Level Cytokine Activity Prediction
and Estimation

H. Robert Frost

genesetCytoSig function

<dl><dt>cytokine.eval</dt>
<dd>Cytokine(s) associated with the query.</dd>
<dt>file.name</dt>
<dd>List of XML file(s) associated with the cytokine(s) beginning with the specific cytokine name.</dd></dl>

Arguments

CytoSig gene set construction. — genesetCytoSig

<dl>

<dt>cytokine.eval</dt>
<dd>Cytokine(s) associated with the query.</dd>


<dt>file.name</dt>
<dd>List of XML file(s) associated with the cytokine(s) beginning with the specific cytokine name.</dd>

</dl>

genesetCytoSig: CytoSig gene set construction.

Description

Usage

Value

Arguments

Examples