import_mothur_otulist: Import mothur list file and return as list object in R.

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

Import mothur list file and return as list object in R.

Description

This is a user-available module of a more comprehensive function for importing OTU clustering/abundance data using the mothur package. The list object returned by this function is not immediately useable by other phyloseq functions, and must be first parsed in conjunction with a separate mothur "group" file. This function is made accessible to phyloseq users for troubleshooting and inspection, but the link{import_mothur()} function is suggested if the goal is to import the OTU clustering results from mothur into phyloseq.

Usage

import_mothur_otulist(mothur_list_file, cutoff=NULL)

Arguments

mothur_list_file

The list file name and/or location as produced by mothur.

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. 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.

Value

A list, where each element is a character vector of 1 or more sequence identifiers, indicating how each sequence from the original data is clustered into OTUs by mothur. Note that in some cases this is highly dependent on the choice for cutoff.

See Also

show_mothur_cutoffs, import_mothur

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