fix: add more logging statemens to sleuth-diffexp.R, add QuantSeq testing data to get QuantSeq tests to pass
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…ile in sleuth-diffexp.R
…ents back into main PR branch
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Maybe we should also refactor the |
dlaehnemann
changed the title
sleuth-diffexp.Rsleuth-diffexp.R, add QuantSeq testing data to get QuantSeq tests to pass
…s, as is usual, so no more str_to_title() conversion is needed in the fgsea.R script
…llapsePathways() to avoid ctlab/fgsea#98
dlaehnemann
merged commit 17d272a
into
fix-canonical-transcript-mapped-read-extraction
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The underlying problem that we identified with the work on this
debug-vroombranch was a malformattedcustomfile for specifying canonical transcript to use insleuth-diffexp.R. The take-away message here were:sleuth-diffexp.Rscript with its largewrite_results()function was hard to debug, and to ease the burden a bit in the future, we should probably keep the extra logging statements we included.datavzrd/diffexp-template.yamldoes not seem to play nice withcustomcanonical transcript files. Thecanonicalcolumn does not make sense in thegenes_aggregatedresults table (as this should only contain gene names / identifiers, and no transcript identifiers, and only the latter could be canonical or not), so we remove it there. However, how to have acanonicalcolumn in thegenes_representativecase with acustomcanonical transcript file still needs to be solved before merging this PR.