import_mothur_groups: Parse mothur group file into a simple hash table.

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

Parse mothur group file into a simple hash table.

Description

The data.frame object returned by this function is not immediately useable by other phyloseq functions, and must be first parsed in conjunction with a separate mothur "list" 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. You will need both a group file and a list file for that end.

Usage

import_mothur_groups(mothur_group_file)

Arguments

mothur_group_file

A character string indicating the location of the mothur-produced group file in which the sample-source of each sequence is recorded. See http://www.mothur.org/wiki/Make.group

Value

A data.frame that is effectively a hash table between sequence names and their sample source.

See Also

import_mothur

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