OTUtable (version 1.1.2)

clean_TaxAss_taxonomy: Clean Taxonomy File Output by TaxAss Workflow

Description

Formats a taxonomy file output by the McMahon Lab TaxAss 16S classification workflow (github.com/McMahonLab/TaxAss) into the same format produced by clean_mothur_taxonomy(). It will also check for and remove OTUs in the taxonomy file that are not in OTU table - this may be the case if rarefaction was performed after classification, as was used in the NTL-Microbial Observatory dataset.

Usage

clean_TaxAss_taxonomy(taxonomy_file, table, remove_bootstrap)

Arguments

taxonomy_file

A .taxonomy file output by the TaxAss workflow

table

An OTU table containing OTU numbers as row names

remove_bootstrap

TRUE or FALSE: if TRUE, removes bootstrap values from the classification strings

Value

Returns the taxonomy with OTUs as row names and seven columns containing each taxonomic level (Kingdom, Phylum, Class, Order, Lineage, Clade, and Tribe)

Examples

# NOT RUN {
# Example path only: path <- "TaxAss_output/bogs.taxonomy"
# table <- clean_shared("mothur_output/bogs.shared", trim.names = T)
# taxonomy <- clean_TaxAss_taxonomy(path, table, remove_bootstrap = F)

# }