Extracts CDS regions from a GTF annotation file or data frame using genomic coordinates and retrieves corresponding DNA sequences from a BSgenome reference.
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.
Value
A data frame containing CDS annotations with corresponding sequences. If save_fasta = TRUE, also writes a FASTA file.
Examples
if (FALSE) { # \dontrun{
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)
}
} # }