extract_element_by_strand: Extract Genomic Elements by Strand

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

Extract Genomic Elements by Strand

Description

Filters a data frame or GTF/GFF3 file to extract specific genomic elements (genes, transcripts, exons, or introns) located on a specified DNA strand (+ or -).

Usage

extract_element_by_strand(input, type, strand, verbose = TRUE)

Arguments

input	A data frame derived from a GTF/GFF3 file or containing genomic annotations.
type	A character string specifying the type of element to extract. Valid options: "gene", "transcript", "exon", "intron".
strand	A character string indicating the DNA strand to filter. Valid options: "+" (forward) or "-" (reverse).
verbose	A logical indicating whether to print the count of extracted elements. Defaults to TRUE.

Details

This function filters the input data based on the type and strand columns. It is useful for strand-specific analyses, such as studying antisense transcripts or strand-biased genomic features.

Value

A data frame containing only the elements of the specified type located on the chosen strand.

Examples

# Example 1: Extract genes on the forward strand using gencode.v1
file_v1 <- system.file("extdata", "gencode.v1.example.gtf.gz", package = "GencoDymo2")
gtf_v1 <- load_file(file_v1)
forward_genes_v1 <- extract_element_by_strand(gtf_v1, type = "gene", strand = "+")

# Example 2: Extract exons on the reverse strand using gencode.v1
reverse_exons_v1 <- extract_element_by_strand(gtf_v1, type = "exon", strand = "-")

GencoDymo2 documentation built on June 8, 2025, 10:29 a.m.