How to fix the error in "meshes" package?
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@mahmoodamiri225-15213
Last seen 3.5 years ago

Hi everyone: I tried to run following codes to compute Semantic Similarity Matrix (SSM) using different measure, combine, database and category to find the best estimate,but in some cases I got an error as follow. I some cases I didn't get the error. here is an example that I got the error:

 

meshdata <- meshdata(MeSHDb="MeSH.Osa.eg.db", category="D", computeIC=T, database="gene2pubmed")
geneID1=c('4326141','4325700','4338366','4342837','4352144','4326138',
          '4328054','4342814','107275659','4327762','4325477','4337260',
          '4332420','4326139','4343995','107276434','4344818','4325681',
          '4344645','4352213','4341304','4328060','9268025','9268534',
          '4331193','4332399','4325948','4341406','4332364','4337643',
          '4347074','4338683','4326570','4340840','4339975','4351983',
          '4338278','4340742','4349385','4336126')
geneID2=c('4340663','4340742','4340766','4340664','4333617','107275499',
          '4329977','4341882','4338366','4331441','4349599','4338742',
          '107275485','4332781','4340658','9268333','4338129','4325949',
          '4341584','4337260','4329976','4349405','4330391','4330463',
          '4332420','4340773','4345898','4350031','107276434','4350837',
          '4332595','4340770','4351088','4351956','4352587','4328054',
          '4349544','4345081','9270392','4335780','4350867','4341611',
          '4340839','4325948','4340840','4336148','4345956','107275659',
          '4330477','4336126')
SSM_rice=geneSim(geneID1=geneID1, geneID2 = geneID2, measure =   "Resnik", combine = "BMA",semData=meshdata)
Error in infoContentMethod_cpp(ID1, ID2, .anc, IC, method, ont) : 
  Expecting a string vector: [type=NULL; required=STRSXP].
In addition: Warning message:
  In `[.data.frame`(meshtbl, meshtbl$meshID %in% id, "parent") :
  restarting interrupted promise evaluation

in addition when I reduced the number of the gene to 10 and 20 for geneID1 and geneID1, respectively, the problem solved, but I need to use all genes. See the following codes:

geneID1=geneID1[1:10]
geneID2=geneID2[1:20]
SSM_rice=geneSim(geneID1=geneID1, geneID2 = geneID2, measure =   "Resnik", combine = "BMA",semData=meshdata)
SSM_rice[1:6,1:6]

 

4340663 4340742 4340766 4340664 4333617 107275499
4326141    0.13      NA    0.13    0.13    0.13        NA
4325700    0.13      NA    0.13    0.13    0.13        NA
4338366    0.13      NA    0.13    0.13    0.13        NA
4342837    0.13      NA    0.13    0.13    0.13        NA
4352144    0.13      NA    0.13    0.13    0.13        NA
4326138    0.13      NA    0.13    0.13    0.13        NA

I'm using R version 3.4.3 (2017-11-30), ‘meshes’ version 1.4.0 and Bioconductor 3.6.

Thanks in advance!

meshes R bioconductor software error • 390 views
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