translate cMD1 paper analyses to cMD3

[lwaldron]

This will replace issue waldronlab/curatedMetagenomicData#70

See https://github.com/waldronlab/curatedMetagenomicData/tree/legacy/vignettes/extras for code to move over.

This is intended as a learning exercise and will be interesting to see how these analyses have changed since the original publication, but there's no need to reproduce something that is too difficult, or to maintain old code if there's an easier way to do it.

[lwaldron]

This is not high priority but I still think it would be a good learning exercise. @cmirzayi it might actually be even more immediately relevant to you if you feel you have the bandwidth? It involves some unsupervised analysis and machine learning using cMD, and there is already code that just needs to be updated to the cMD3 API.

[zhangy2361]

Thank you and your team for developing the package. I have encountered some confusion when using this package. Firstly, whether the relative abundance table has been standardized and does not need to consider the batch of the study？ Is this the final relative abundance table?
Secondly, I downloaded a cancer data from different studies using curatedMetagenomicData, and whether the study factor needs to be considered when finding the significantly different microbiome using massLin. Or, what other analysis methods for finding the significantly different microbiome are recommended when using curatedMetagenomicData? Or, do I need to follow this tutorial (vignettes/Sex_metaanalysis_vignette.Rmd). Looking forward to your reply.