export_env_file: Export environment (ENV) file for UniFrac Server.

In phyloseq: Handling and analysis of high-throughput microbiome census data

Description

Creates the environment table that is needed for the original UniFrac algorithm. Useful for cross-checking, or if want to use UniFrac server. Optionally the ENV-formatted table can be returned to the R workspace, and the tree component can be exported as Nexus format (Recommended).

Usage

export_env_file(physeq, file = "", writeTree = TRUE, return = FALSE)

Arguments

physeq	(Required). Experiment-level (phyloseq-class) object. Ideally this also contains the phylogenetic tree, which is also exported by default.
file	(Optional). The file path for export. If not-provided, the expectation is that you will want to set return to TRUE, and manipulate the ENV table on your own. Default is "", skipping the ENV file from being written to a file.
writeTree	(Optional). Write the phylogenetic tree as well as the the ENV table. Default is TRUE.
return	(Optional). Should the ENV table be returned to the R workspace? Default is FALSE.

Examples

# # Load example data
# data(esophagus)
# export_env_file(esophagus, "~/Desktop/esophagus.txt")

phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.