Add differential expression #50
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Managed to poke around in RStudio 🎉
Can step through the test files adequately.
Tried to set debug(differentialExpression) and couldn't step through the actual "setMethod" function. Will try to figure this out.
Sending these comments now so they don't get lost!
| # The comparator must be ordinal, binary, or categorical | ||
| groupAValues <- getGroupLabels(comparator, "groupA") | ||
| groupBValues <- getGroupLabels(comparator, "groupB") | ||
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Should we check that groupAValues and groupBValues are mutually exclusive?
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In fact we already do! The check is in the class-Comparator.R file. So someone can't even create a Comparator object to give to our function if the groupAValues and groupBValues overlap.
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| result <- differentialExpression(testCollection, comparator=comparatorVariable, method='DESeq', verbose=F) | ||
| expect_equal(length(result@droppedColumns), 0) | ||
| dt <- result@data |
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So this is a 288 row table with one column - SampleID.
Is this useful for anything? If it had a second column with groupA/B membership, maybe it would?
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So this is a 288 row table with one column - SampleID.
Yup!
Is this useful for anything? If it had a second column with groupA/B membership, maybe it would?
It's not being used right now, but it's supposed to help us tell the user which samples get thrown out in the computation because of bad data or whatever the reason. I like the idea of adding the groupA/groupB membership there. Not sure yet where it would be used, but when the need comes I'm glad to know we. have a natural place to add that information.
Yay I worked it out. |
The goal is to get the current implementation of deseq up and running. Improvements should be a new issue/PR
To Dos:
Decided to leave microbiomeComputations totally alone. We can update its imports and such at a later date but for now they're left alone. The only update it would need is to import
deseqfrom veupathutils (and it's classes and such). It should also use veupathUtils's default floors.