mp_import_qiime: Import function to load the output of qiime.

In YuLab-SMU/MicrobiotaProcess: A comprehensive R package for managing and analyzing microbiome and other ecological data within the tidy framework

Import function to load the output of qiime.

Description

The function was designed to import the output of qiime and convert them to MPSE class.

Usage

mp_import_qiime(
  otufilename,
  mapfilename = NULL,
  otutree = NULL,
  refseq = NULL,
  ...
)

Arguments

otufilename	character, the file contained otu table, the ouput of qiime.
mapfilename	character, the file contained sample information, the tsv format, default is NULL.
otutree	treedata, phylo or character, the file contained reference sequences, or treedata object, which is the result parsed by functions of treeio, default is NULL.
refseq	XStringSet or character, the file contained the representation sequence file or XStringSet class to store the representation sequence, default is NULL.
...	additional parameters.

Value

MPSE-class.

Author(s)

Shuangbin Xu

YuLab-SMU/MicrobiotaProcess documentation built on Nov. 8, 2024, 4:37 p.m.