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(high-temp) No 3. Filtering: (16S rRNA/ITS) Output

dataset
posted on 06.05.2022, 13:45 authored by Jarrod ScottJarrod Scott
Output files from the No 3. Filtering Workflow page of the SWELTR high-temp study. ASV filtering for 16S rRNA & ITS using a) Arbitrary filtering, b) PERFect (PERmutation Filtering test for microbiome data), and c) PIME (Prevalence Interval for Microbiome Evaluation) Workflow objects:

filtering_wf.rdata: contains all variables and phyloseq objects from 16s rRNA and ITS ASV filtering. To see the Objects, in R run load("filtering_wf.rdata", verbose=TRUE)

Additional files:

For convenience, we also include individual phyloseq objects for each filtered data set.

Arbitrary:
ssu18_ps_filt.rds: phyloseq object for Arbitrary filtered 16S rRNA ASVs.
its18_ps_filt.rds:
phyloseq object for Arbitrary filtered ITS ASVs.

PERfect:

ssu18_ps_perfect.rds: phyloseq object for PERfect filtered 16S rRNA ASVs.
its18_ps_perfect.rds:
phyloseq object for PERfect filtered ITS ASVs.

PIME:

ssu18_ps_pime.rds: phyloseq object for PIME filtered 16S rRNA ASVs.
its18_ps_pime.rds: phyloseq object for PIME filtered ITS ASVs.

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

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