OTU_time_series-class: Time series class for OTU tables

In AlmaasLab/micInt: Find microbial interactions

Time series class for OTU tables

Description

This class provides a way to integrate measurements of time to OTU tables, useful for time series analysis

Usage

OTU_time_series(table, time_points)

## S4 method for signature 'data.frame,numeric'
OTU_time_series(table, time_points)

## S4 method for signature 'phyloseq,numeric'
OTU_time_series(table, time_points)

## S4 method for signature 'otu_table,numeric'
OTU_time_series(table, time_points)

## S4 method for signature 'phyloseq,character'
OTU_time_series(table, time_points)

Arguments

table	A refined table returned form refine_data, an experiment level phyloseq object or a phyloseq otu_table.
time_points	A numeric vector of the start point. If an experiment level phyloseq object is provided, it can be a character vector of length one, specifying which column in the sample data to use for the time points.

Details

If you provide an experiment level phyloseq object, you might want to split it into groups before using the constructor function.

Slots

table

Data frame, the refined OTU table representing the community

time_points

Numeric, the time from the start of the experiment or any other arbitrary time reference

Examples

library(micInt)
library(phyloseq)
data("seawater")
subsetted_seawater <- subset_samples(seawater, Reactor == 2)
OTU_time_series(subsetted_seawater,"Week")

AlmaasLab/micInt documentation built on April 1, 2022, 10:37 a.m.