GencoDymo2 (version 1.0.2)

extract_cds_sequences: Extract Coding Sequences (CDS) from GTF Annotations

Description

Extracts CDS regions from a GTF annotation file or data frame using genomic coordinates and retrieves corresponding DNA sequences from a BSgenome reference.

Usage

extract_cds_sequences(input, genome, save_fasta, output_file, verbose)

Value

A data frame containing CDS annotations with corresponding sequences. If save_fasta = TRUE, also writes a FASTA file.

Arguments

input

A character string (GTF file path) or GRanges object containing CDS annotations.

genome

A BSgenome object for the relevant genome (e.g., BSgenome.Hsapiens.UCSC.hg38).

save_fasta

Logical indicating whether to save sequences to a FASTA file.

output_file

Character string specifying the FASTA output path.

verbose

Logical indicating whether to print progress messages.

Examples

if (FALSE) {
if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly = TRUE)) {
  suppressPackageStartupMessages(library(GenomicRanges))
  genome <- BSgenome.Hsapiens.UCSC.hg38::BSgenome.Hsapiens.UCSC.hg38
  file_v1 <- system.file("extdata", "gencode.v1.example.gtf.gz", package = "GencoDymo2")
  gtf_v1 <- load_file(file_v1) # Should return GRanges
  cds_seqs <- extract_cds_sequences(gtf_v1, genome, save_fasta = FALSE)
}
}