ngsLCA_profile: Generate a Combined Taxa Profile

View source: R/ngsLCA_profile.R

ngsLCA_profileR Documentation

Generate a Combined Taxa Profile

Description

Read lca files in the appointed directory to generate a combined taxa profile named "complete_profile.txt" in folder "path/run/taxonomic_profiles/".

Usage

ngsLCA_profile(path, run = "run01", remove.sample = NULL, metadata = NULL)

Arguments

path

working directory, which should contain lca files that will be processed.

run

run name, a folder that will be created for storing generated files and results; default is "run01".

remove.sample

a comma separated vector listing file names indicating samples that will NOT be included for analysis, optional.

metadata

path to sample metadata, optional. The metadata should be a tab separated txt file, with the first column being lca file names, 2nd column being sample ID (sample names will be shown in the generated files), and 3rd column being age, depth, or the rank of samples (will be used for ordering samples in the generated files; must be numeric). An example for metadata can be found at 'system.file("extdata","sample_metadata.txt",package="ngsLCA")'.

Value

A combined taxa profile named by complete_profile.txt.

Examples

ngsLCA_profile(path=system.file("extdata","lca_files",package="ngsLCA"),
               run="run01",
               metadata=system.file("extdata","sample_metadata.txt",package="ngsLCA"))

## This will combine all lca files in "path/" to generate a file
## named "complete_profile.txt" in path/run01/taxonomic_profiles",
## with replacing the file names by sample names supplied in
## "sample_metadata.txt".



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