CytoSig gene set construction. — genesetCytoSig • scaper

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)
#>       gene weight cytokine
#> 1    ABCA1  1.375      IL6
#> 2    ABCB4 -0.922      IL6
#> 3    ABCC2  1.868      IL6
#> 4    ABCD2 -1.379      IL6
#> 5  ABHD17C -1.141      IL6
#> 6     ABI3  1.783      IL6
#> 7    ACAT2 -1.366      IL6
#> 8    ACKR3 -1.195      IL6
#> 9     ACO1  0.811      IL6
#> 10   ACOX3  2.891      IL6