ngsLCA_filter: Filter the Combined Taxa Profile

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

Filter the Combined Taxa Profile

Description

Filter the combined taxa profile. Running this function will update the existing "complete_profile.txt".

Usage

ngsLCA_filter(
  path,
  run = "run01",
  remove.taxa = NULL,
  threshold.1 = 2,
  threshold.2 = 0,
  threshold.3 = 5
)

Arguments

path	working directory, same to ngsLCA_profile.
run	name of the run, default is "run01".
remove.taxa	a list of NCBI taxaID indicating taxa that will be removed. This can be a comma separated vector or the path to a text file listing one taxaID in each line.
threshold.1	minimum reads number required for confirming a taxon in each sample; default is 2.
threshold.2	minimum read percentage (to the total reads number of a given sample) required for confirming a taxon in each sample, ranging from 0 to 1; default is 0.
threshold.3	minimum sum of reads across all samples required for confirming a taxon in the combined taxa profile; default is 5.

Value

An updated complete_profile.txt (after taxa filters).

Examples

ngsLCA_filter(path=system.file("extdata","lca_files",package="ngsLCA"),
              run="run01",
              remove.taxa="1115501,10114",
              threshold.1=2,
              threshold.2=0,
              threshold.3=2)


## This will filter and update the combined taxa profile:
## "path/run01/taxonomic_profiles/complete_profile.txt"
## by the 3 thresholds supplied, and by removing taxa
## with taxaID 1115501 and 10114.

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