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gmelloni / PrecisionTrialDrawer

A set of tools to help bioinformaticians, clinicians and biostatisticians to design, analyze and finalize a custom gene panel for clinical trial in cancer genomics.
GNU General Public License v3.0
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better error message when no alteration to display #2

Open alessando-guida opened 6 years ago

alessando-guida commented 6 years ago

When data one alteration type are missing from the TCGA, the package returns a generic message:

"No alteration to display for the selected tumor types and alteration types"

It would be more useful to specify what alteration data are missing. For example if fusion data are missing:

No fusion alteration data to display for the selected tumor types

gmelloni commented 6 years ago

It's kind of complicated to solve. there are 2 filters applied: tumor_type and alterationType. If it's a alterationType problem, a warning should appear earlier, saying:

toBeBind <- object@dataSubset[alterationType]
checkDataExistance <- sapply(toBeBind , is.null)
if(any(checkDataExistance)){
    warning("No data for" %++% paste(names(toBeBind)[checkDataExistance] , collapse=", ") %+% ". They will be removed from alterationType")
    alterationType <- alterationType[!checkDataExistance]
    }

The message you refer to can appear for 2 reasons:

In the second case... who is to blame? mutations? copynumber? fusions? I don't know... The only thing I can add is a summary of the sample size according to the intersection of the multi omics data maybe 🤔