import_env_file: Read a UniFrac-formatted ENV file.

In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

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/

See Also

import

tip_glom

Examples

# import_env_file(myEnvFile, myTree)

joey711/phyloseq documentation built on Nov. 4, 2022, 1:16 a.m.