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microbiome / mia

Microbiome analysis
https://microbiome.github.io/mia/
Artistic License 2.0
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MAE helper methods #388

Open antagomir opened 1 year ago

antagomir commented 1 year ago

The MAE sample names are not always in sync (same samples, different order; or only partially overlapping samples)

This may lead to situations where one has to align sample sorting manually: mae[[1]] <- mae[[1]][, colnames(mae[[2]])]

It might be handy to have a helper methods that could automatically align the samples between different MAEs, like: mae <- align_mae(mae, keep="shared")

This would ensure that the shared samples have the same ordering across all MAE. It could also include arguments to decide what to do with non-overlapping samples.

The role of colLinks (links between samples in different experiments) should be explored.

Existence of possible other available methods should be checked.

Use of terminology aligned with dplyr (bind_cols etc) could be considered as well.

antagomir commented 1 year ago

In principle, an entirely new package "MAEtools" would be useful for generic MAE manipulation.. but that's a whole other story again. Perhaps some others have interest to implement such thing as well.