phyloseq: import_mothur – R documentation

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import_mothur

General function for importing mothur data files into phyloseq.

Description

Technically all parameters are optional, but if you don't provide any file connections, then nothing will be returned. While the list and group files are the first two arguments for legacy-compatibility reasons, we don't recommend that you use these file types with modern (large) datasets. They are comically inefficient, as they store the name of every sequencing read in both files. The mothur package provides conversions utilities to create other more-efficient formats, which we recommend, like the shared file for an OTU table. Alternatively, mothur also provides a utility to create a biom-format file that is independent of OTU clustering platform. Biom-format files should be imported not with this function, but with import_biom. The resulting objects after import should be identical in R.

Usage

import_mothur(mothur_list_file = NULL, mothur_group_file = NULL,
  mothur_tree_file = NULL, cutoff = NULL, mothur_shared_file = NULL,
  mothur_constaxonomy_file = NULL,
  parseFunction = parse_taxonomy_default)

Arguments

`mothur_list_file`	(Optional). The list file name / location produced by mothur.
`mothur_group_file`	(Optional). The name/location of the group file produced by mothur's `make.group()` function. It contains information about the sample source of individual sequences, necessary for creating a species/taxa abundance table (`otu_table`). See `http://www.mothur.org/wiki/Make.group`
`mothur_tree_file`	(Optional). A tree file, presumably produced by mothur, and readable by `read_tree`. The file probably has extension `".tree"`.
`cutoff`	(Optional). A character string indicating the cutoff value, (or `"unique"`), that matches one of the cutoff-values used to produce the OTU clustering results contained within the list-file created by mothur (and specified by the `mothur_list_file` argument). The default is to take the largest value among the cutoff values contained in the list file. If only one cutoff is included in the file, it is taken and this argument does not need to be specified. Note that the `cluster()` function within the mothur package will often produce a list file with multiple cutoff values, even if a specific cutoff is specified. It is suggested that you check which cutoff values are available in a given list file using the `show_mothur_cutoffs` function.
`mothur_shared_file`	(Optional). A shared file produced by mothur.
`mothur_constaxonomy_file`	(Optional). A consensus taxonomy file produced by mothur.
`parseFunction`	(Optional). A specific function used for parsing the taxonomy string. See `parse_taxonomy_default` for an example. If the default is used, this function expects a semi-colon delimited taxonomy string, with no additional rank specifier. A common taxonomic database is GreenGenes, and in recent versions its taxonomy entries include a prefix, which is best cleaved and used to precisely label the ranks (`parse_taxonomy_greengenes`).

Value

The object class depends on the provided arguments. A phyloseq object is returned if enough data types are provided. If only one data component can be created from the data, it is returned.

FASTER (recommended for larger data sizes):

If only a mothur_constaxonomy_file is provided, then a taxonomyTable-class object is returned.

If only a mothur_shared_file is provided, then an otu_table object is returned.

SLOWER (but fine for small file sizes):

The list and group file formats are extremely inefficient for large datasets, and they are not recommended. The mothur software provides tools for converting to other file formats, such as a so-called “shared” file. You should provide a shared file, or group/list files, but not both at the same time. If only a list and group file are provided, then an otu_table object is returned. Similarly, if only a list and tree file are provided, then only a tree is returned (phylo-class).

References

http://www.mothur.org/wiki/Main_Page

Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Examples

# # The following example assumes you have downloaded the esophagus example
# # dataset from the mothur wiki:
# # "http://www.mothur.org/wiki/Esophageal_community_analysis"
# # "http://www.mothur.org/w/images/5/55/Esophagus.zip"
# # The path on your machine may (probably will) vary
# mothur_list_file  <- "~/Downloads/mothur/Esophagus/esophagus.an.list"
# mothur_group_file <- "~/Downloads/mothur/Esophagus/esophagus.good.groups"
# mothur_tree_file  <- "~/Downloads/mothur/Esophagus/esophagus.tree"
# # # Actual examples follow:
# show_mothur_cutoffs(mothur_list_file)
# test1 <- import_mothur(mothur_list_file, mothur_group_file, mothur_tree_file)
# test2 <- import_mothur(mothur_list_file, mothur_group_file, mothur_tree_file, cutoff="0.02")
# # Returns just a tree
# import_mothur(mothur_list_file, mothur_tree_file=mothur_tree_file)
# # Returns just an otu_table
# import_mothur(mothur_list_file, mothur_group_file=mothur_group_file)
# # Returns an error
# import_mothur(mothur_list_file)
# # Should return an "OMG, you must provide the list file" error
# import_mothur()

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