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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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getExperimentCrossAssociation to ignore 0s? #390

Open antagomir opened 1 year ago

antagomir commented 1 year ago

In ecological studies the association analyses are sometimes carried out only for those samples that have observations (of a given species for instance).

It would be useful to allow association analyses, ignoring zeroes in one or both data sets via an additional argument.

This is also not straightfwd to do before calling the correlation function since different features may have observations in different samples. Automation would take user a long way.

This applies especially between associations of taxa (to other taxa, or other omics / phenotypes).

antagomir commented 1 year ago

Some literature refs on this aspect of ecological studies could be added in manpage reference list.