nciTable {sigora}

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.

Source

<https://github.com/NCIP/pathway-interaction-database/tree/master/download>

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)