filter_taxonomy {phylotypr} | R Documentation |
Filter taxonomy
Description
The filter_taxonomy()
function will filter a consensus taxonomy to remove
any taxonomic levels where the confidence score is below a min_confidence
level
Usage
filter_taxonomy(consensus, min_confidence = 80)
Arguments
consensus |
A list object that contains two slots each with an equal
sized vector. The |
min_confidence |
A double value between 0 and 100 (default = 80). The minimum percentage of bootstrap replicates that had the same classification. Any confidence score below this value will have the corresponding taxonomy removed |
Value
A list object containing two equally sized vectors that are filtered
to remove low confidence taxonomies. One vector, taxonomy
,
contains the taxonomy at each taxonomic level and the other vector,
confidence
contains the confidence score for that taxonomy. There
will be no taxonomies or confidence scores below min_confidence
Examples
oscillospiraceae <- list(
taxonomy = c(
"Bacteria", "Bacillota", "Clostridia",
"Eubacteriales", "Oscillospiraceae",
"Flintibacter"
),
confidence = c(100, 100, 99, 99, 98, 58)
)
filter_taxonomy(oscillospiraceae, min_confidence = 80)