sigora (version 3.2.0)

nciTable: NCI human gene-pathway associations.

Description

PID-NCI human pathway repository, as a data frame with three columns corresponding to : pathwayId , pathwayName, gene. This is an example of the expected format for the input data to makeGPS.

Details

This dataset is provided to illustrate how to create your own GPS repositories.nciTable is a dataframe with threecolumns corresponding to pathwayId, pathwayName and gene. Each row describes the association between an individual gene and a PID-NCI pathway. As you see in the examples, section, one can convert this dataframe to a GPS repository using makeGPS, and save the results for future reuse. Using the thus created GPS repository one can preform Signature Overrepresentation Analysis on lists of genes of interest.

Examples

data(nciTable)
nciH <- makeGPS(pathwayTable = load_data("nciTable"))
data(idmap)
ils <- grep("^IL", idmap[, "Symbol"], value = TRUE)
ilnci <- sigora(
  queryList = ils, GPSrepo = nciH, level = 3
)