Add missing functions to OMA

[antagomir]

In data import section, mention that also these functions from mia package are available to import data from different formats. No example needed, just the name:

• makeTreeSummarizedExperimentFromDADA2, makeSummarizedExperimentFromBiom
• loadFromMetaphlan
• readQZA

In the same chapter where MDS / PCoA examples are given, also mention that the following are available (I will then modify further). Also add the full name there (JSD = Jensen-Shannon divergence etc.). The names can be found from the function manpages. No examples needed to OMA for these.

• calculateJSD, runJSD
• calculateNMDS, plotNMDS
• calculateCCA, runCCA
• calculateRDA, runRDA
• calculateOverlap, runOverlap
• calculateDPCoA, runDPCoA

In the data manipulation chapter, mention that data can be rarified with:

• subsampleCounts (rarification) -> section on "Library size"!
• also add a citation to this paper (see the function manpage for 1-2 sentences of explanation,I think it already cites this paper): https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003531

Section on Quality Control, mention:

• isContaminant, isNotContaminant
• addContaminantQC, addNotContaminantQC

Just mention these as well, with at most 1 sentence description:

• mapTaxonomy -> section on Tidying and subsetting
• getPrevalentAbundance (abundance of prevalents) -> section on Prevalence
• getRareTaxa, subsetByRareTaxa -> section on Prevalence
• mergeRows (mergeCols) -> section on Tidying and subsetting
• getUniqueTaxa -> section on Top Taxa
• bestDMNFit -> mention in Dirichlet Multinomial Mixture section
• performDMNgroupCV -> add later; mention in Dirichlet Multinomial Mixture section
• estimateDivergence -> in section on beta diversity

[RiboRings]

What if I added the links to the corresponding man pages? For instance:

Other functions

• makeTreeSummarizedExperimentFromDADA2
• loadFromMetaphlan
• readQZA