Replace getExperiment* and testExperiment* functions with getCrossAssociation

microbiome / mia

Microbiome analysis

https://microbiome.github.io/mia/

Artistic License 2.0

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Replace getExperiment* and testExperiment* functions with getCrossAssociation #511

Closed thpralas closed 4 months ago

thpralas commented 5 months ago

Create new function getCrossAssociation to replace the following :

getExperimentCrossAssociation
getExperimentCrossCorrelation
testExperimentCrossAssociation
testExperimentCrossCorrelation

New function getCrossAssociation makes the significance test as default (test_significance default value is TRUE)

TuomasBorman commented 5 months ago

Looks good, the idea of this PR was to remove additional functions that we have only one function for cross-correlation. Moreover, the name of function was shortened

TuomasBorman commented 5 months ago

test_significance could still be FALSE by default. The function uses base (or stats) R by default for calculating cross-correlation. The function that calculates correlation without significance testing is much faster

antagomir commented 5 months ago

Some conflicts..?

antagomir commented 5 months ago

Otherwise seems fine