MeSH enrichment analysis with "meshes"
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ayatrience • 0
@ayatrience-19286
Last seen 2.5 years ago

I wanted to do MeSH enrichment analysis with "meshes" package designed by Guangchuang YU. However, I entered like below following description of "meshes" in R,

result <- enrichMeSH(gene = degsentrez, universe = allentrez, MeSHDb = "MeSH.db",database = "Gendoo",category = "A", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff =0.05)

error messages come; "no such column: GENEID".

What is wrong with my code? Degsentrez & allentrez are column vector of entrez gene ID as description requires I think.

meshes • 468 views
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what's the output of traceback() immediately run after the error appear?

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This is the output.

16: stop(list(message = "no such column: GENEID", call = resultcreate(conn@ptr, statement), cppstack = list(file = "", line = -1L, stack = "C++ stack not available on this system"))) 15: resultcreate(conn@ptr, statement) 14: initialize(value, ...) 13: initialize(value, ...) 12: new("SQLiteResult", sql = statement, ptr = resultcreate(conn@ptr, statement), conn = conn, bigint = conn@bigint) 11: .local(conn, statement, ...) 10: dbSendQuery(conn, statement, ...) 9: dbSendQuery(conn, statement, ...) 8: .local(conn, statement, ...) 7: dbGetQuery(x$conn, query) 6: dbGetQuery(x$conn, query) 5: .local(x, keys, columns, keytype, ...) 4: select(db, keys = database, columns = c("GENEID", "MESHID", "MESHCATEGORY"), keytype = "SOURCEDB") 3: select(db, keys = database, columns = c("GENEID", "MESHID", "MESHCATEGORY"), keytype = "SOURCEDB") 2: getMeSH_data(MeSHDb, database, category) 1: enrichMeSH(gene = degs.entrez[, 2], universe = all.entrez[, 2], MeSHDb = "MeSH.db", database = "Gendoo", category = "A", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.05)

but, perhaps I can do that correctly, when I change to the MeSH.db for mice "MeSH.Mmu.eg.db" and database = "gendoo" it seems to work correctly and I can get something like result by head().

Thank you very much for your answer and sorry for troubling you if this comes from my lack of knowledge of R language.

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