import_mothur_dist: Import mothur-formatted distance file

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

Description

The mothur application will produce a file containing the pairwise distances between all sequences in a dataset. This distance matrix can be the basis for OTU cluster designations. R also has many built-in or off-the-shelf tools for dealing with distance matrices.

Usage

import_mothur_dist(mothur_dist_file)

Arguments

mothur_dist_file

Required. The distance file name / location produced by mothur.

Value

A distance matrix object describing all sequences in a dataset.

See Also

import_mothur

Examples

# # Take a look at the dataset shown here as an example:
# # "http://www.mothur.org/wiki/Esophageal_community_analysis"
# # find the file ending with extension ".dist", download to your system
# # The location of your file may vary
# mothur_dist_file <- "~/Downloads/mothur/Esophagus/esophagus.dist"
# myNewDistObject  <- import_mothur_dist(mothur_dist_file)

Example output

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