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I keep getting the following error message when running

maf <- readMaf(mafFile = "project_maf/C2.maf.tsv", 
               clinicalFile = clin.File, 
               ccfFile = NULL, 
               refBuild = "hg19")

Error message:

>Error in dplyr::left_join(): ! Join columns must be present in data. ✖ Problem with Tumor_Sample_Barcode. Run rlang::last_error() to see where the error occurred.

Currently using MesKit to perform this analysis which requires me to analysis one maf per sample. This means there's only one Tumor_Sample_Barcode per maf file.

Does anyone have any ideas on how to overcome this error?

(http://bioconductor.org/packages/release/bioc/vignettes/MesKit/inst/doc/MesKit.html#4_Start_with_the_Maf_object)

colnames(maf.tb)

     [1] "Hugo_Symbol"            "Chromosome"             "Start_Position"        
 [4] "End_Position"           "Variant_Classification" "Variant_Type"          
 [7] "Reference_Allele"       "Tumor_Seq_Allele2"      "Ref_allele_depth"      
[10] "Alt_allele_depth"       "VAF"                    "Tumor_Sample_Barcode" 
        
          
`colnames.clin.tb`
               
Tumor_Sample_Barcode Tumor_ID Patient_ID Tumor_Sample_Label
CH1374
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    The code shows your dataset doesn't have any common names for joining – akrun Jan 29 '23 at 22:30
  • Welcome to Stack Overflow. It's easier to help if you [make this question reproducible](https://stackoverflow.com/questions/5963269/how-to-make-a-great-r-reproducible-example) by including small representative datasets in a plain text format, and all of the relevant code. We can't see what columns are in the two datasets, nor the details of the left join. – neilfws Jan 29 '23 at 22:36
  • Post output from `str(clin.file)` and `str( read.delim("project_maf/C2.maf.tsv") )` – IRTFM Jan 29 '23 at 22:40
  • You have not posted structure information that matches the parameters you are giving to `MesKit::readMaf`. I wonder if the `MesKit::readMaf` function is as well tested as the `maftools::read.maf` function? – IRTFM Jan 30 '23 at 01:46

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