Implement Feature Abundance Cut-off

azmfaridee / mothur

This is GSoC2012 fork of 'Mothur'. We are trying to implement a number of 'Feature Selection' algorithms for microbial ecology data and incorporate them into mother's main codebase.

https://github.com/mothur/mothur

GNU General Public License v3.0

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Implement Feature Abundance Cut-off #36

Open azmfaridee opened 11 years ago

azmfaridee commented 11 years ago

Implement feature abundance cut-off, the current feature rank is quire exhaustive and a bit distracting, it'd be nice to see a subset of top ranking features either depending on a fixed number or fixed percentage.

kdiverson commented 11 years ago

I'm getting very different feature ranking with the GSoC HMP data https://www.dropbox.com/s/2gmla3xk76xom8e/Stool.0.03.subsample.0.03.filter.shared.zip

outputs: https://gist.github.com/kdiverson/5636774

EDIT: my initial R features were not sorted, see plot below. Mothur output is still missing Otu19349 and Otu19310

kdiverson commented 11 years ago

Sorted features from R