ggmRSCU (version 0.1.0)

read_mega: Process MEGA CSV Files

Description

Reads and processes MEGA-generated CSV files from a specified directory, extracts codon usage data, and returns a consolidated dataset.

Usage

read_mega(folder_path)

Value

A data frame containing:

AA

Amino acid abbreviation

Codon

DNA codon sequence

Fill

Position index within amino acid group

Species

Species identifier from file name

RSCU

Calculated Relative Synonymous Codon Usage value

Arguments

folder_path

Path to directory containing MEGA CSV files. Files should follow MEGA format with columns for Codon, Count, and RSCU values.

Details

Processes files through these steps:

1. Identifies valid header lines containing "Codon", "Count", and "RSCU"

2. Extracts codon/amino acid data below headers

3. Calculates position indices (Fill) for synonymous codons

4. Combines all species data into a single data frame

Examples

# Using example data
example_dir <- system.file("extdata", "mega", package = "ggmRSCU")
result <- read_mega(example_dir)
head(result)