Extract gene sequences from a GTF/GFF annotation file and corresponding genome FASTA. This function parses the annotation file to get gene coordinates and extracts sequences from the genome FASTA file.
Usage
extract_known_genes(
gtf_file,
genome_fasta,
feature_type = "gene",
gene_attribute = "gene_id",
min_length = 300,
max_genes = Inf
)Arguments
- gtf_file
Character string specifying the path to the GTF/GFF file
- genome_fasta
Character string specifying the path to the genome FASTA file
- feature_type
Character string specifying the feature type to extract (default: "gene", alternatives: "exon", "CDS", "transcript")
- gene_attribute
Character string specifying the gene ID attribute (default: "gene_id")
- min_length
Minimum gene length in base pairs (default: 300)
- max_genes
Maximum number of genes to extract (default: Inf)
Examples
if (FALSE) { # \dontrun{
# Extract gene sequences from GTF and genome files
known_genes <- extract_known_genes(
gtf_file = "annotations.gtf",
genome_fasta = "genome.fasta",
min_length = 300
)
# Create reference profile
ref_profile <- create_reference_profile(known_genes)
} # }