clean_mothur_taxonomy {OTUtable}

Clean mothur-format Taxonomy File

Description

Reduces information in a mothur .taxonomy file by removing the second column with the number of reads per OTU. 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. This function was formerly clean_taxonomy in v1.0.0.

Usage

clean_mothur_taxonomy(taxonomy_file, table, remove_bootstrap)

Arguments

taxonomy_file

A .taxonomy file output by mothur

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 <- "mothur_output/bogs.taxonomy"
# table <- clean_shared("mothur_output/bogs.shared", trim.names = T)
# taxonomy <- clean_mothur_taxonomy(path, table, remove_bootstrap = F)