Issues trying to load example data sets from cbio curated data sets

[mjafin]

Hi there,
Thank you for this super useful package @arsenij-ust, much appreciated. I'm trying to get to grips with using the tool but have come across a few issues. Perhaps it's got to do with cBio data format updates - would love to hear your thoughts.

Just to test cbpManager I downloaded two data sets from https://www.cbioportal.org/datasets :

• laml_tcga_pan_can_atlas_2018
• dlbc_tcga_pan_can_atlas_2018

The AML data set loads OK-ish but the Patient tab throws an error:
You specified the columns: PATIENT_ID, but the column names of the data are TCGA-AB-3008, LAML, LAML, , , , , , , , , , , , , , , , , , , , , , , , , , Yes, 1:DECEASED, 27.02436138, , , , , ,
Upon inspection of the R error it points to 105: exprFunc [...cbpManager/reactives/reactivesPatientTab.R#39]

The DLBCL data set crashes the app with the error Warning: Error in scan: line 2 did not have 38 elements

Any thoughts on what might be causing these issues?

Separately: If I create a new study from scratch, will it be compatible with the current latest release of cBioPortal?

[arsenij-ust]

Dear @mjafin,
Thanks for reporting these errors, I will have a look and try to fix this.

Best regards
Arsenij