Question: GO similarity by GOSemSim
gravatar for ahatashkar
5 weeks ago by
ahatashkar0 wrote:


I am using GOSemSim package for GO similarity calculation. I have a list of Uniprot gene IDs. My dataset is S. cerevisiae. so I code as below:

hsGO2 <- godata('', keytype = "UNIPROT", ont="MF", computeIC=FALSE)

genes <- c("P25044", "P40454", "P32901", "P43606")

mgeneSim(genes, semData=hsGO2, measure="Wang", combine="BMA", verbose=FALSE)

but after that, I just get this answer: 

Error in go_matrix[gos[[i]], gos[[j]]] : incorrect number of dimensions

Please help me. Thank you

ADD COMMENTlink written 5 weeks ago by ahatashkar0

> select(, keys = genes, "GO", keytype = "UNIPROT")
Error in .testForValidKeys(x, keys, keytype, fks) :
  None of the keys entered are valid keys for 'UNIPROT'. Please use the keys method to see a listing of valid arguments.
> genes
[1] "P25044" "P40454" "P32901" "P43606"
ADD REPLYlink written 4 weeks ago by Guangchuang Yu1.0k
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