main: Handle full microsatellite analysis from command-line

In ShawHahnLab/microsat: Computational, High-throughput Individual Identification through Microsatellite Profiling

Handle full microsatellite analysis from command-line

Description

A small wrapper function to read a configuration file path from command-line arguments, load the configuration data (see load_config), and run full_analysis.

Usage

main(args = NULL)

Arguments

args	optional character vector of arguments to use rather than those detected with base::commandArgs.

Value

list of results, with the full configuration list included as "config."

Examples

## Not run: 
# Set up a temporary copy of the CHIIMP test data
example_dir <- tempfile()
dir.create(example_dir)
setwd(example_dir)
test_data$write_seqs(test_data$seqs,
                     "str-dataset",
                      "Replicate1-Sample%s-%s.fasta")
locus_attrs_path <- system.file("example_locus_attrs.csv",
                                package = "chiimp")
file.copy(locus_attrs_path, "locus_attrs.csv")
# Run the example analysis
config_path <- system.file("example_config.csv", package = "chiimp")
results <- main(config_path)

## End(Not run)

ShawHahnLab/microsat documentation built on Aug. 25, 2023, 11:16 p.m.