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tgirke / systemPipeR

Project Website:
http://girke.bioinformatics.ucr.edu/systemPipeR
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overLapper invalid class error #14

Closed shyamrallapalli closed 5 years ago

shyamrallapalli commented 5 years ago

Hi I got a bit of perplexing issue with overLapper function I have many list of vectors ranging from 2 to 10 that i am trying to get intersect matrix in a large pipeline and on one instance that error-ed I got 2 vectors and for some reason overLapper fails with an error i am not sure i understand

I have tested with a smaller vectors and seem to have no issue with it. Post my code here, if this could be a bug.

myList = list()
myList[["List1"]] = c("108", "1123", "1271", "1316", "1317", "1360", "1361", "1583", "1615", "1631",
 "1722", "1872", "1873", "191", "2060", "210", "2156", "22", "2260", "290", "351", "375", "447",
 "451", "461", "463", "680", "689", "708", "828", "888", "895")
myList[["List2"]] = c("1127", "117", "1180", "1207", "1222", "1271", "1316", "1317", "1360", "1615",
 "1722", "175", "1873", "191", "194", "2104", "2156", "24", "290", "31", "322", "409", "447", "461",
 "463", "650", "661", "680", "689", "69", "748", "888")

overLapper(myList, type="vennsets")
Error in validObject(.Object) : 
  invalid class “VENNset” object: invalid object for slot "vennlist" in class "VENNset": got class "matrix", should be or extend class "list"
myList = list()
myList[["List1"]] = c("108", "1123", "1271", "1316", "1317", "1360", "1361")
myList[["List2"]] = c("1127", "117", "1180", "1207", "1222", "1271", "1316")

overLapper(myList, type="vennsets")
An instance of 'VENNset' with 2 label sets
tgirke commented 5 years ago

This was a bug for a very rare input case. Thanks for reporting it. I have committed a fix for it on GitHub and Bioc (Version 1.17.6).