phyloseq_subset: Make a list of phyloseq object subsets

In nick-youngblut/HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

Description

Create a list of phyloseq object subsets based on phyloseq sample data parameters (e.g., a phyloseq subset for each treatment)

Usage

phyloseq_subset(physeq, params, ex)

Arguments

physeq	Phyloseq object
params	data.frame of parameters supplies to ex
ex	Expression for subsetting the phyloseq object

Value

A list of Phyloseq objects

Examples

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

nick-youngblut/HTSSIP documentation built on May 23, 2019, 4:46 p.m.