| clean_TaxAss_taxonomy {OTUtable} | R Documentation |
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)
Author(s)
Alexandra Linz <amlinz16@gmail.com>
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)