HTSSIP (version 1.4.1)

get_treatment_params: Get parameters for subsetting the phyloseq dataset

Description

This function is needed if you want to make multiple subsets of the phyloseq object in order to make specific comparisons between isotopically labeled-treatments and

Usage

get_treatment_params(physeq, exp_params, treatment = NULL)

Arguments

physeq

Phyloseq object

exp_params

a vector listing the columns in the phyloseq sample_data table that can subset the phyloseq dataset in order to make the specific labeled-treatment vs labeled-control comparisons that you would like to make.

treatment

This is an expression used to filter out the control-specific parameters (if needed).

Details

their corresponding controls (eg., from the same time point).

Makes a data.frame of all of the parameter values that differ among the treatment-control comparisons.

For example, if you want to compare the gradient fractions from each labeled-treatment to its corresponding unlabeled-Control (both from the same time point).

Examples

# NOT RUN {
data(physeq_S2D2)
# Here, the treatment/controls (12C & 13C) are listed in substrate,
# and should be matched by 'Day'. The 13C-treatments can be identified by
# the expression: "Substrate != '12C-Con'"
get_treatment_params(physeq_S2D2, c('Substrate', 'Day'), "Substrate != '12C-Con'")

# }