genesetCytoSig: CytoSig gene set construction.

In scaper: Single Cell Transcriptomics-Level Cytokine Activity Prediction and Estimation

CytoSig gene set construction.

Description

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.

Usage

genesetCytoSig(cytokine.eval, file.name)

Arguments

cytokine.eval	Cytokine(s) associated with the query.
file.name	List of XML file(s) associated with the cytokine(s) beginning with the specific cytokine name.

Value

Dataframe consisting of genes and the associated log2 fold change values associated with the specific cytokine(s).

Examples

file.name.cytosig1 <- system.file("extdata", "IL6_output.csv", package = "scaper")
genesetCytoSig(cytokine.eval = "IL6", file.name = file.name.cytosig1) %>% head(10)

scaper documentation built on April 17, 2025, 1:07 a.m.