get_treatment_params: Get parameters for subsetting the phyloseq dataset

Description Usage Arguments Details Examples

View source: R/phyloseq_subset.R

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

1
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

1
2
3
4
5
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'")

HTSSIP documentation built on May 15, 2018, 9:03 a.m.