import_otutab_taxa: Import USEARCH otutab_taxa File into phyloseq
In jfq3/RDPutils: R Utilities for Processing RDPTool Output
Description
Usage
Arguments
Details
Value
Author(s)
Examples
View source: R/import_otutab_taxa.R
Description
Converts USEARCH's usearch_global output option otutabout to a phyloseq object with otu_table and tax_table.
Usage
1
import_otutab_taxa(in_file)
Arguments
in_file
An otutab_taxa file generated by USEARCH 8.1+
Details
The USEARCH usearch_global function has an option to output an OTU table with taxonomy assignments in a tab-delimited text file. The output resembles the legacy QIIME format. This function imports such a file into a phyloseq object with otu_table and tax_table.
Value
A phyloseq object with otu_table and tax_table.
Author(s)
John Quensen
Examples
1
2
##---- Not run. ----
##-- expt <- import_otutab_taxa(in_file = "otutab_taxa_03.txt")
jfq3/RDPutils documentation built on Nov. 8, 2019, 1:05 p.m.
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Description Usage Arguments Details Value Author(s) Examples
View source: R/import_otutab_taxa.R
Description
Converts USEARCH's usearch_global output option otutabout to a phyloseq object with otu_table and tax_table.
Usage
1 | import_otutab_taxa(in_file)
|
Arguments
in_file |
An otutab_taxa file generated by USEARCH 8.1+ |
Details
The USEARCH usearch_global function has an option to output an OTU table with taxonomy assignments in a tab-delimited text file. The output resembles the legacy QIIME format. This function imports such a file into a phyloseq object with otu_table and tax_table.
Value
A phyloseq object with otu_table and tax_table.
Author(s)
John Quensen
Examples
1 2 | ##---- Not run. ----
##-- expt <- import_otutab_taxa(in_file = "otutab_taxa_03.txt")
|
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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