Studies Structural Variant Chart Title Wording
Miu ki Yip
Hello,
We are running a local version of cBioPortal v6.3.2 and we would like to know if there is a way to make a change locally or if there was a workaround for this behavior that we are seeing.
The homepage of studies that contains charts and graphs has a chart labeled “Structural Variant Genes (X profiled samples)”. We noticed that this chart takes into consideration only samples that contains found structural variant in the data file but not all the samples listed in the cases list file that we provide for structural variants. The wording suggests to viewers that only these samples that appear are profiled for structural variants. However, all the samples listed in the cases list are profiled for structural variants, but some were found to not have any. Is there any way to change this wording in the chart title to either say something like “Structural Variant Genes (X found samples)” or to replace X in “Structural Variant Genes (X profiled samples)” with the number of samples in the case list?
We notice that the case list for structural variants do get loaded into the database, so the information is available:
Finished recaching...
--> stable ID: study_sv
--> sample list name: Samples with SV data
--> number of samples in file: 20
--> number of samples stored in final sample list : 20
Thank you!
Jessica Singh
Hi Miu ki,
The denominator shown in that chart is driven by the gene panel matrix file. If that file does not indicate that all samples were profiled for structural variants, the portal will only count samples with detected SV events.
Could you update the gene panel matrix file to reflect that all 20 samples were profiled and then refresh the study? That should populate the chart with the correct denominator.
Please let us know if that resolves the issue. If you have any follow-up questions, please reply to all so the conversation is captured on the forum.
Best,
Jessica
Jessica Singh - Schedule a Meeting with me
Solutions Consultant - Genomics and Target Discovery Team
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