genesetReactome: Reactome gene set construction.

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

Reactome gene set construction.

Description

Returns the gene set consisting of genes on the Reactome pathway hierarchy given input cytokine(s) and specified list of pathway hierarchy xml file(s) with file name beginning with the specified cytokine (i.e., 'IL6_Interleukin6_signaling.xml') as currently provided for the IL6 cytokine.

Usage

genesetReactome(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 list of genes on the molecular pathway associated with the specified cytokine(s).

Examples

file.name.reactome1 <- system.file("extdata", "IL6_Interleukin6_signaling.xml", 
package = "scaper")
genesetReactome(cytokine.eval = "IL6", file.name = file.name.reactome1) %>% head(10)

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