clean_mothur_taxonomy: Clean mothur-format Taxonomy File

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

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)

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