Requested new features for MARS

[trjhensen]

Hi, here are my requested features. Tables 4 and 5 are nice to haves, for now but I would be very interested in being able to better investigate influences on mapping as any statistics on just the relative abundances are technically violate IID, making it not usable for any real comparative statistics. Performing a centered-log ratio transformation should enable such comparisons.

Best,
Tim

Features:

1. A table with information on all species read counts in the microbiome with the following columns:
   a. Species name
   b. Flag if a species was mapped or unmapped
   c. Mean (SD) of relative abundances (mapped & unmapped reads)
   d. Mean (SD) of relative abundances (mapped reads)
   e. Mean (SD) of relative abundances (unmapped reads)

2. A table with information on the relative phylum abundances in the mapped and unmapped reads with the following columns:
   a. Phylum name
   b. Mean (SD) of phylum level reads (mapped + unmapped)
   c. Mean (SD) of phylum level reads (mapped)
   d. Mean (SD) of phylum level reads (unmapped)

3. A table with the number of species, genera, families, orders, classes, phyla, and kingdoms in the mapped reads, unmapped reads and mapped & unmapped reads.

4. A table with information on all species in the microbiome with the following columns:
   a. Species name
   b. Flag if a species was mapped or unmapped
   c. Mean (SD) of centered-log ratio transformed abundances (mapped & unmapped reads)
   d. Mean (SD) of centered-log ratio transformed abundances (mapped reads)
   e. Mean (SD) of centered-log ratio transformed abundances (unmapped reads)

5. A table with information on all phyla in the microbiome with the following columns:
   a. Phylum name
   c. Mean (SD) of centered-log ratio transformed abundances (mapped & unmapped reads)
   d. Mean (SD) of centered-log ratio transformed abundances (mapped reads)
   e. Mean (SD) of centered-log ratio transformed abundances (unmapped reads)