nciTable.RdPID-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.
<https://github.com/NCIP/pathway-interaction-database/tree/master/download>
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.
data(nciTable) nciH<-makeGPS(pathwayTable=load_data('nciTable')) #> Time difference of 0.8909671 secs data(idmap) ils<-grep("^IL",idmap[,"Symbol"],value=TRUE) ilnci<-sigora(queryList=ils,GPSrepo=nciH,level=3) #> [1] "Mapped identifiers from Symbol to Ensembl.Gene.ID ..." #> pathwy.id description pvalues Bonferroni successes #> 1 il23pathway IL23-mediated signaling events 5.494e-64 1.049e-61 36.27 #> 2 il27pathway IL27-mediated signaling events 3.164e-34 6.043e-32 18.14 #> 3 il12_2pathway IL12-mediated signaling events 3.188e-12 6.089e-10 13.20 #> 4 il1pathway IL1-mediated signaling events 1.115e-09 2.130e-07 8.42 #> 5 il4_2pathway IL4-mediated signaling events 1.070e-05 2.044e-03 9.03 #> PathwaySize N sample.size #> 1 172.95 46257.95 93.08 #> 2 65.51 46257.95 93.08 #> 3 420.16 46257.95 93.08 #> 4 156.05 46257.95 93.08 #> 5 687.89 46257.95 93.08