Extract Splice Site Motifs for MaxEntScan Analysis (5' or 3')

Extracts donor (5') or acceptor (3') splice site motifs from a genomic dataset using BSgenome sequences.

Usage

extract_ss_motif(input, genome, type, verbose, save_fasta, output_file)

Arguments

input

A data frame with columns: seqnames, strand, intron_start, intron_end, transcript_id, intron_number.

genome

A BSgenome object (e.g., from BSgenome.Hsapiens.UCSC.hg38).

type

One of "5ss" (donor) or "3ss" (acceptor).

verbose

Logical; print progress messages.

save_fasta

Logical; write a FASTA file of extracted motifs.

output_file

Name/path of the output FASTA file.

Value

A data frame including extracted splice site motifs.

See also

assign_splice_sites, df_to_fasta

Examples

if (FALSE) { # \dontrun{
if (requireNamespace("BSgenome.Hsapiens.UCSC.hg38", quietly = TRUE)) {
  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)
  introns <- extract_introns(gtf_v1)
  motifs_df <- extract_ss_motif(introns, genome, "5ss", verbose = FALSE)
}
} # }