import_otu_table: import otu table function

In DeepSubsurfer/demmogorgon: What the Package Does (One Line, Title Case)

Description

This function reads your data file, formats sample ID's and taxa names, and converts absolute abundances to relative abundances. The otu table must contain "otu" in the file name with sample ID's as column names and taxa as row names.#'the metadata file must have "meta" in the file name and contain matching sample ID's to the otu table in the first column. To format date, there must be a column named "date" in the metadata file.

Usage

import_otu_table(normalize = TRUE, add_metadata = TRUE,
  format_date = TRUE)

Arguments

normalize	argument to normalize data to relative abundance, defaults to TRUE
add_metadata	argument to normalize data to relative abundance, defaults to TRUE
format_date	argument to normalize data to relative abundance, defaults to TRUE

Examples

import_otu_table(normalize=TRUE, add_metadata=TRUE, format_date=TRUE) #returns dataframe of normalized otu table with added metadata
import_otu_table(normalize=FALSE) #returns otu table with absolute abundances

DeepSubsurfer/demmogorgon documentation built on June 5, 2019, 7:56 a.m.