CreatePhyloseqObj: Function to recreate phyloseq object
In xia-lab/MicrobiomeAnalystR: MicrobiomeAnalystR - A comprehensive R package for statistical, visual, and functional analysis of the microbiome.
CreatePhyloseqObj R Documentation
Function to recreate phyloseq object
Description
This function recreates the phyloseq object.
Usage
CreatePhyloseqObj(mbSetObj, type, taxa_type, taxalabel, isNormInput)
Arguments
mbSetObj
Input the name of the mbSetObj.
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 jeff.xia@mcgill.ca
McGill University, Canada
License: GNU GPL (>= 2)
xia-lab/MicrobiomeAnalystR documentation built on April 17, 2024, 7:45 p.m.
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| CreatePhyloseqObj | R Documentation |
Function to recreate phyloseq object
Description
This function recreates the phyloseq object.
Usage
CreatePhyloseqObj(mbSetObj, type, taxa_type, taxalabel, isNormInput)
Arguments
mbSetObj |
Input the name of the mbSetObj. |
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 jeff.xia@mcgill.ca McGill University, Canada License: GNU GPL (>= 2)
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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