clean_TaxAss_taxonomy: Clean Taxonomy File Output by TaxAss Workflow

In OTUtable: North Temperate Lakes - Microbial Observatory 16S Time Series Data and Functions

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)

Author(s)

Alexandra Linz <[e-mail]>

Examples

# 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)

OTUtable documentation built on May 1, 2019, 10:51 p.m.