import_mothur_otu_table: Import mothur list and group files and return an otu_table
In joey711/phyloseq: Handling and analysis of high-throughput microbiome census data

import_mothur_otu_table

R Documentation

Import mothur list and group files and return an otu_table

Import mothur list and group files and return an otu_table

import_mothur_otu_table(mothur_list_file, mothur_group_file, cutoff=NULL)

`mothur_list_file`	The list file name and/or location as produced by mothur.
`mothur_group_file`	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`
`cutoff`	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.

An otu_table object.