read_mega {ggmRSCU} | R Documentation |
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)
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:
Identifies valid header lines containing "Codon", "Count", and "RSCU"
Extracts codon/amino acid data below headers
Calculates position indices (Fill) for synonymous codons
Combines all species data into a single data frame
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
Examples
# Using example data
example_dir <- system.file("extdata", "mega", package = "ggmRSCU")
result <- read_mega(example_dir)
head(result)
[Package ggmRSCU version 0.1.0 Index]