Description Usage Arguments Value Examples
Create a list of phyloseq object subsets based on phyloseq sample data parameters (e.g., a phyloseq subset for each treatment)
1 | phyloseq_subset(physeq, params, ex)
|
physeq |
Phyloseq object |
params |
data.frame of parameters supplies to |
ex |
Expression for subsetting the phyloseq object |
A list of Phyloseq objects
1 2 3 4 5 6 7 8 9 | data(physeq_S2D2)
# making subsets by substrate and time point
params = get_treatment_params(physeq_S2D2, c('Substrate', 'Day'))
# filtering out controls
params = dplyr::filter(params, Substrate!='12C-Con')
# making expression for subsetting labeled-unlabeled gradient comparisons
ex = "(Substrate=='12C-Con' & Day=='${Day}') | (Substrate=='${Substrate}' & Day == '${Day}')"
physeq_l = phyloseq_subset(physeq_S2D2, params, ex)
physeq_l
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