CreatePhyloseqObjMeta: Function to recreate phyloseq object in meta-analysis module

In xia-lab/MicrobiomeAnalystR: MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.

Function to recreate phyloseq object in meta-analysis module

Description

This function recreates the phyloseq object.

Usage

CreatePhyloseqObjMeta(
  mbSetObj,
  dataName,
  type,
  taxa_type,
  taxalabel,
  isNormInput
)

Arguments

mbSetObj	Input the name of the mbSetObj.
dataName	Input the file name of selected dataset
type	Input the format of the uploaded files. "text" for .txt or .csv files, "biom" for .biom, and "mothur" for mothur files.
taxa_type	Input the taxonomy labels. "SILVA" for SILVA taxonomy, "Greengenes" for Greengenes taxonomy, "QIIME" for QIIME taxonomy, "GreengenesID" for Greengenes OTU IDs, and "Others/Not_specific" for others.
taxalabel	Logical, T if taxonomy labels were already included in the OTU table and F if not.

Author(s)

Jeff Xia [e-mail] McGill University, Canada License: GNU GPL (>= 2)

xia-lab/MicrobiomeAnalystR documentation built on April 17, 2024, 7:45 p.m.