ngsLCA_rank: Classify Taxa to Taxonomic Ranks

In wyc661217/ngsLCA: Process and Visualize Lca Files and Taxonomic Profiles

Classify Taxa to Taxonomic Ranks

Description

Classify the combined taxa profile (and grouped taxa profiles generated by ngsLCA_group if available) into user-defined taxonomic ranks. Results will be in "path/run/taxonomic_profiles/taxa_ranks/".

Usage

ngsLCA_rank(path, run = "run01", rank.name = "species,genus,family")

Arguments

path	working directory, same to ngsLCA_profile.
run	name of the run, default is "run01".
rank.name	a comma separated vector listing the taxonomic ranks that will be used for classifying taxa profiles; default is "species,genus,family"

Value

Taxa profiles clustered into taxa ranks.

Examples

ngsLCA_rank(path=system.file("extdata","lca_files",package="ngsLCA"),
            run="run01",
            rank.name="species,genus")


## This will classify the combined taxa profile (and
## grouped taxa profiles if available) of "run01" into
## species and genus, by merging all taxa below a species
## into that species, and all taxa below a genus into
## that genus. Generated files will be in
## "path/run01/taxonomic_profiles/taxa_ranks/".

wyc661217/ngsLCA documentation built on June 2, 2025, 12:02 a.m.