Question: GOHyperGParams GOstats R package - categorySubsetIds parameter
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gravatar for salamandra
2.3 years ago by
salamandra240
salamandra240 wrote:

Hi all,

I want to know which GO ids of a group of pre-selected GO ids are enriched. I used the categorySubsetIds parameter of GOHyperGParams to do this. However the number of GO ids got is much higher than the number of pre-selected GO ids.

A toy example follows (GOslim is the list of pre-selected GOids):

A <- c("86", "51412", "192669", "8289", "57492", "83858", "10533", "10538", "54880", "1230", "947", "79577", "55038", "64866", "1017", "1026", "1063", "1105", "91851", "55118") 

B <- c("79624", "23192", "85003", "151887", "7555", "9267", "8663", "3692", "51359", "90625", "28982", "2597", "81502", "57470", "4223", "57380", "57552", "54539", "55655", "199713", "79031", "123", "5558", "10635", "81892")

allgenes <- c(A,B)
GO.slim <- c("GO:0000003", "GO:0000278", "GO:0000902", "GO:0002376", "GO:0003013", "GO:0005975")

paramsGO <- new("GOHyperGParams", geneIds = A[A %in% allgenes], universeGeneIds = allgenes, annotation = "org.Hs.eg.db", ontology = "BP", testDirection = "over", categorySubsetIds = GO.slim) 
hypGO <- hyperGTest(paramsGO)
hypGO
tgo <- summary(hypGO, pvalue = 1.1)
nrow(tgo) # number of GO ids much higher than number of elements in GO.slim

I know I can select them afterwards of doing hyperGTest, but am curious how to properly use the parameter categorySubsetIds

ADD COMMENTlink written 2.3 years ago by salamandra240
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