get_treatment_params: Get parameters for subsetting the phyloseq dataset

In nyoungb2/HTSSIP: High Throughput Sequencing of Stable Isotope Probing Data Analysis

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

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'")

nyoungb2/HTSSIP documentation built on May 24, 2019, 11:51 a.m.