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bigomics / playbase

Core back-end functionality and logic for OmicsPlayground
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CRITICAL: Remove artifacts from xbioc probe type results #114

Closed mauromiguelm closed 3 months ago

mauromiguelm commented 3 months ago

This pull request removes artifacts from the xbioc probe type results. The changes include removing empty columns and ".nuID" from the idtypetable.

before

Browse[1]> idtype.table

            .nuID GENEBANK 
     856       37      107 
Browse[1]> names(which.max(idtype.table))
[1] ""

table returned "" as a valid probe type, as it had 856 matches compared to 107 for GENEBANK.

after fix

Browse[2]>     idtype.table <- gsub(".nuID", NA, idtype.table)
Browse[2]>     idtype.table <- idtype.table[which(idtype.table != "")]
Browse[2]> 
Browse[2]>     idtype.table <- table(idtype.table)
Browse[2]> names(which.max(idtype.table))
[1] "GENEBANK"

GENEBANK is then converted to UNIPROT, which gives correct probe type.