MesKit error message - Join columns must be present in data.

Question

[CH1374]

I keep getting the following error message when running

maf <- readMaf(mafFile = maf.File,
              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.

Have checked the maf file and all the headings match the required headings.

colnames(maf.File)
 [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"

clin.File includes

Tumor_Sample_Barcode
Tumor_ID
Patient_ID
Tumor_Sample_Label

Anyone have any ideas how to overcome this error?

[zx8754]

Error is clear, can you provide the column names project_maf/C2.maf.tsv ?

[CH1374]

column names for the maf are:

[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"

(have updated this above as well :))

[zx8754]

OK, so you do have "Tumor_Sample_Barcode" in both datasets. Post as an issue at github: https://github.com/Niinleslie/MesKit/issues

[bataibence]

When you use a custom variants text file (instead of an original maf) it gives the same error message if the data is space separated (such as standard with e.g. in R with readr::write_delim). It should be tab separated, which solves the issue.