Reactome gene set construction.

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)
#>     gene cytokine
#> 1   JAK1      IL6
#> 2  IL6ST      IL6
#> 3    IL6      IL6
#> 4   IL6R      IL6
#> 5   JAK2      IL6
#> 6   TYK2      IL6
#> 7    JAK      IL6
#> 8  STAT1      IL6
#> 9  STAT3      IL6
#> 10  STAT      IL6