Leo Lahti

Extend transformAssay so that it accepts multiple transformations at once? In addition to `transformAssay(tse, ..., method="clr")` we could have `transformAssay(tse, ..., method=c("relabundance", "clr", "log10"), pseudocount=TRUE)` i.e. method could also be...

Revise naming conventions across the mia framework

1

The naming conventions for functions and arguments should be systematically evaluated (mia vs other mia packages vs SCE etc) See at least these issues for a starting point: - #338...

merge and cluster: separate or unified functions for rows / cols?

1

We have now: Clustering in a single function, with the `MARGIN` argument: - `cluster(... , MARGIN="features")` - `cluster(... , MARGIN="samples")` -> This function returns a \code{SummarizedExperiment} with clustering information in...

Batch transformations.

1

Create Function to add given transformation to all altExps / ranks at once, or at least provide an example in OMA/mia. This is handy also since methods like `agglomerateFeaturesByRank` or...

perSampleDominantFeatures works only with taxonomyRanks

1

The perSampleDominantFeatures and addPerSampleDominantFeatures This works: ``` library(mia) data(GlobalPatterns, package="mia") tse

Metaphlan & counts

5

The metaphlan pipeline is providing only the relative abundance assay, and not counts. This is sometimes inconvenient for various standard metagenomic analysis methods and workflows that expect counts. The curatedMetagenomicData...

Consider feature / sample agglomeration methods as useful dimension reduction methods. First issue to consider is whether it is necessary to have separate functions for Features vs. Samples, or could...

altExp support for meltAssay

2

It is not possible to choose altExp for meltAssay currently. One can however call `meltAssay(altExp(tse, ...))` to do this for any altExp. Perhaps this is enough and there is no...

Absolute vs. relative abundances

11

Some microbiome studies are starting to report measures of absolute abundance in addition to sequencing read counts and relative abundances. The `MicrobiomeExperiment` could/should support incorporating this information, too.

calculateAitchison

19

I propose to add a function `calculateAitchison`. This would be similar to `calculateUnifrac` but it will not require tree and it will return Aitchison distances. These are defined as Euclidean...