How to fix the error in meshes package?

Question

[mahmood.amiri225]

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!

[Ram]

Please add the values for geneID1 and geneID2.

[mahmood.amiri225]

I edited the codes and put the geneID1 and geneID2 valuse.

[cpad0112]

mahmood.amiri225 39 entry in geneID1 seems to be problematic and try removing it, Try running for 39 and it will fail:

geneSim(geneID1=geneID1[39], geneID2 = geneID2, measure ="Resnik", combine = "BMA",semData=meshdata)

and

geneSim(geneID1=geneID1[40], geneID2 = geneID2, measure ="Resnik", combine = "BMA",semData=meshdata)
geneSim(geneID1=geneID1[c(1:38,40)], geneID2 = geneID2, measure ="Resnik", combine = "BMA",semData=meshdata)

If it fails for 39, then see if there is an extra space at the end of 39 entry

Answer 1

[Ram]

I'm looking at examples here: http://bioconductor.org/packages/release/bioc/vignettes/meshes/inst/doc/meshes.html and it seems that you're using semData=datahsamd whereas you should be using semData=meshdata and also follow up with a data(meshdata) after your first line of code.

[mahmood.amiri225]

Thank you for mentioning the mistake. This is not the exact problem. I only made a mistake when I tried to make a question! In my running codes I used semData=meshdata