(high-temp) No 4. Taxonomic: (16S rRNA/ITS) Output

**Output files from the No 4. Taxonomic Workflow** page of the SWELTR high-
temp study. In this workflow we used the microeco package for taxonomic
assessment. We first converted each phyloseq object into a microtable object
using the file2meco package.

**taxa_wf.rdata** : contains all variables and phyloseq objects from 16s rRNA
and ITS ASV taxonomic assessment. To see the Objects, in R run
_load("taxa_wf.rdata", verbose=TRUE)_

Additional files:

For convenience, we also include individual phyloseq and microtable objects
(collected in zip files).

_I_** _TS (its_taxa_objects.zip)_ :**
**its18_ps_work_me.rds** : microtable object for the FULL (unfiltered) ITS
data.
**its18_ps_filt_me.rds** : microtable object for the Arbitrary filtered ITS
data.
**its18_ps_perfect_me.rds** : microtable object for the PERfect ITS data.
**its18_ps_pime_me.rds** : microtable object for the PIME ITS data.

_**16S rRNA (ssu_taxa_objects.zip):**_
**ssu18_ps_work_me.rds** : microtable object for the FULL (unfiltered) 16S
rRNA data.
**ssu18_ps_filt_me.rds** : microtable object for the Arbitrary filtered 16S
rRNA data.
**ssu18_ps_perfect_me.rds** : microtable object for the PERfect 16S rRNA data.
**ssu18_ps_pime_me.rds** : microtable object for the PIME 16S rRNA data.

For one of the 16S rRNA analyses we looked at family-level diversity of major
bacterial phyla. For this analysis, we renamed NA ranks by the next highest
named rank. For example, ASV13884 was unclassifed at family level, so the _NA_
was replaced with the next highest named rank (in this case order). Therefore
the family-level classification for this ASV was changed to _o_Polyangiales_.
Doing this allowed us to include uncalssifed abundance in our analyses. We
include the following phyloseq objects containing the modifed taxonomies.

**ssu18_ps_work_clean.rds** : modified phyloseq object for the FULL
(unfiltered) 16S rRNA data.
**ssu18_ps_filt_clean.rds** : modified phyloseq object for the Arbitrary
filtered 16S rRNA data.
**ssu18_ps_perfect_clean.rds** : modified phyloseq object for the PERfect
filtered 16S rRNA data.
**ssu18_ps_pime_clean.rds** : modified phyloseq object for the PIME filtered
16S rRNA data.

Source code for the workflow can be found here:
https://github.com/sweltr/high-temp/blob/master/taxa.Rmd