GO similarity by GOSemSim

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ahatashkar • 0

@ahatashkar-16156

Last seen 6.5 years ago

Hi

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('org.Hs.eg.db', 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

gosemsim similarity • 1.3k views

ADD COMMENT • link 6.5 years ago ahatashkar • 0

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> select(org.Hs.eg.db, 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 REPLY • link 6.5 years ago Guangchuang Yu ★ 1.2k

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