phyloseq: import_env_file – R documentation

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import_env_file

Read a UniFrac-formatted ENV file.

Description

Convenience wrapper function to read the environment-file, as formatted for input to the UniFrac server (http://bmf2.colorado.edu/unifrac/). The official format of these files is that each row specifies (in order) the sequence name, source sample, and (optionally) the number of times the sequence was observed.

Usage

import_env_file(envfilename, tree=NULL, sep="\t", ...)

Arguments

`envfilename`	(Required). A charater string of the ENV filename (relative or absolute)
`tree`	(Optional). `phylo-class` object to be paired with the output otu_table.
`sep`	A character string indicating the delimiter used in the file. The default is `"\t"`.
`...`	Additional parameters passed on to `read.table`.

Value

An otu_table-class, or phyloseq-class if a phylo-class argument is provided to tree.

References

http://bmf2.colorado.edu/unifrac/

Examples

# import_env_file(myEnvFile, myTree)

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