MesKit error message - Join columns must be present in data.
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?
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bataibence •
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CH1374 •
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CH1374 •
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Error is clear, can you provide the column names
project_maf/C2.maf.tsv?column names for the maf are:
(have updated this above as well :))
OK, so you do have
"Tumor_Sample_Barcode"in both datasets. Post as an issue at github: https://github.com/Niinleslie/MesKit/issuesWhen 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.