nciTable | R Documentation |
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
.
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.
<https://github.com/NCIP/pathway-interaction-database/tree/master/download>
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)
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