NetORA: The core function to score a signature
In JiantaoShi/NetORA: Network-based pathway over-representation analysis (NetORA)

Description Usage Arguments Value Author(s) References Examples

This function is the core function to test whether a signature is statistically enriched in a pathway in network-level.

1	NetORA(SG, queryTable, PG, FDR = 0.05)

`SG`	a vector of gene signature
`queryTable`	a data frame returned by NetORA_Pre
`PG`	a vector of background genes
`FDR`	an FDR cutoff to define gene that are significantly connected a pathway (defaul 0.05)

a list

Jiantao Shi

Jiantao Shi: NetORA, a package for network-based pathway over-representation analysis.

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)