This function implements a preprocessing step that find all neighbor of a given pathway.
a vector of pathway
a integer matrix which is accepted by NetGPA as a network
a data frame
Jiantao Shi: NetORA, a package for network-based pathway over-representation analysis.
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library("NetORA") data(text_2006_12_NetGPA) data(Example_NetGPA) ExE_Hyper <- Example_NetGPA$ExE_Hyper queryTable <- NetORA_Pre(ExE_Hyper, text_2006_12_NetGPA, progressBar = TRUE) Cancer_GS <- Example_NetGPA$Cancer_GeneSet PG <- colnames(text_2006_12_NetGPA) mergedT <- NetORA_GS(Cancer_GS, queryTable, PG, FDR = 0.05)
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