reannotateTax: reannotateTax

In OxfordCMS/OCMSutility: Utility functions for OCMS

reannotateTax

Description

Reannotate taxonomy

reannotateTax was renamed to reannotate_tax for more consistent function naming nomenclature in OCMSutility. Usage is still exactly the same

Usage

reannotateTax(taxonomy)

Arguments

taxonomy

taxonomy table. Must have c('Kingdom','Phylum','Class','Order','Family','Genus','Species') as columns. unclassified entries are denoted as NA

Value

updated taxonomy table with "unclassified" prepended with higher level classifications

Examples

data(asv_example)
# adding Kingdom column; removing sequence column because don't need asv IDs in this example
old_tax <- tax_example
colnames(old_tax)[1] <- 'Kingdom'
old_tax$Kingdom <- 'Bacteria'
knitr::kable(head(old_tax))

new_tax <- reannotateTax(old_tax)
# ->
new_tax <- reannotate_tax(old_tax)
knitr::kable(head(new_tax))

OxfordCMS/OCMSutility documentation built on Feb. 27, 2025, 8:19 p.m.