Import mothur-formatted distance file
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.
import_mothur_dist(mothur_dist_file)
mothur_dist_file |
Required. The distance file name / location produced by mothur. |
A distance matrix object describing all sequences in a dataset.
# # 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)
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