phyloseq: export_env_file – R documentation

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export_env_file

Export environment (ENV) file for UniFrac Server.

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

Handling and analysis of high-throughput microbiome census data

v1.34.0

AGPL-3

Authors

Paul J. McMurdie <joey711@gmail.com>, Susan Holmes <susan@stat.stanford.edu>, with contributions from Gregory Jordan and Scott Chamberlain

Initial release

2019-04-23