assign_splice_sites: Assign intron donor and acceptor splice sites consensus

In GencoDymo2: Comprehensive Analysis of 'GENCODE' Annotations and Splice Site Motifs

Assign intron donor and acceptor splice sites consensus

Description

This function takes a data frame of intron coordinates and a genome sequence (ideally human or mouse) and returns a data frame with two additional columns for the donor and acceptor splice site consensus sequences. It prepares the donor and acceptor sequences based on the provided intron coordinates and the specified genome (e.g., human hg38), making it useful for downstream analysis of splicing events.

Usage

assign_splice_sites(input, genome, verbose = TRUE)

Arguments

input	A data frame containing intron coordinates.
genome	A BSgenome object like BSgenome.Hsapiens.UCSC.hg38. Must be explicitly passed.
verbose	Logical. If TRUE, the function prints progress messages while preparing the splice site data. Default is TRUE.

Value

A data frame containing the original intron data, with two additional columns:

• donor_ss: The donor splice site consensus sequence for each intron.

• acceptor_ss: The acceptor splice site consensus sequence for each intron.

See Also

extract_introns, find_cryptic_splice_sites

Examples

## Not run: 
  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_df <- extract_introns(gtf_v1)
    result <- assign_splice_sites(introns_df, genome)
  }

## End(Not run)

GencoDymo2 documentation built on Aug. 21, 2025, 5:54 p.m.