ngsLCA_group: Group Taxa in the Combined Taxa Profile

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

Group Taxa in the Combined Taxa Profile

Description

Group the combined taxa profile into user-defined taxa units. Results will be in "path/run/taxonomic_profiles/taxa_groups/".

Usage

ngsLCA_group(
  path,
  run = "run01",
  group.name = "Viruses,Archaea,Bacteria,Fungi,Viridiplantae,Metazoa",
  threshold.perGroup = 0
)

Arguments

path	working directory, same to ngsLCA_profile.
run	name of the run, default is "run01".
group.name	a comma separated vector listing the taxonomic units that will be used for grouping taxa, need to be as the scientific names of NCBI taxonomy <https://www.ncbi.nlm.nih.gov/taxonomy>; default is "Viruses,Archaea,Bacteria,Fungi,Viridiplantae,Metazoa".
threshold.perGroup	minimum reads percentage (to the total reads number of each group) required for confirming a taxon in each group of each sample, ranging from 0 to 1; default is 0.

Value

Taxa profiles grouped into taxa units.

Examples

ngsLCA_group(path=system.file("extdata","lca_files",package="ngsLCA"),
             run="run01",
             group.name="Viridiplantae,Metazoa",
             threshold.perGroup=0.01)

## This will extract all taxa under Viridiplantae and Metazoa
## from the combined taxa profile of "run01", and filter
## these 2 taxa profiles by threshold.perGroup to generate 2
## files named "Viridiplantae.txt" and "Metazoa.txt" in
## "path/run01/taxonomic_profiles/taxa_groups/".

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