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r-bioinformatics / edgePy

A Python implementation of edgeR for differential expression analysis
https://edgepy.readthedocs.io
MIT License
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Testing CPM and a few bugfixes along the way #56

Closed apfejes closed 6 years ago

apfejes commented 6 years ago

Tests the cpm() and resolves a few bugs found while making the test work.

For Code review: Please ignore all of the commits below. I don't want to rebase, and when we squash and merge, they will all disappear. Please just look at the two files changed. The binaries files changing are simply a correction on the sample list to remove the 0th element in the imported data, which is the header, "genes".

apfejes commented 6 years ago

Addresses https://github.com/r-bioinformatics/edgePy/issues/23

apfejes commented 6 years ago

I don't have a problem with it, but we need a stronger design discussion. I think that's probably more useful in interactive python, maybe? I'm not sure why you'd go down that path instead of using this to modify the DGEList.

Carbyne commented 6 years ago

An option could be to imitate numpy, where we have a edgePy.cpm() that returns a new object and edgePy.DGEList.cpm() that modifies the object.

Or maybe imitate pandas with edgePy.DGEList.cpm(inplace=True/False), although this may make type hinting messier?

eegk commented 6 years ago

Seems fine to me.