eliminate_redundant_elements: Eliminate Redundant Genomic Elements

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

Eliminate Redundant Genomic Elements

Description

Removes redundant genomic elements (exons or introns) from a data frame, ensuring each element is uniquely represented. Redundancy is determined by genomic coordinates and gene ID.

Usage

eliminate_redundant_elements(input, element_type = "exon")

Arguments

input	A data frame containing genomic element coordinates (exons or introns) with columns seqnames, start, end, and gene_id.
element_type	The type of genomic element to process. Valid options are "exon" (default) or "intron".

Details

This function uses genomic coordinates (chromosome, start, end) and gene ID to identify and remove duplicate entries. For exons, coordinates are directly compared. For introns, coordinates are derived from intron_start and intron_end columns (check extract_introns function for more details)

Value

A data frame with redundant elements removed, retaining only unique entries based on coordinates and gene ID.

Examples

file_v1 <- system.file("extdata", "gencode.v1.example.gtf.gz", package = "GencoDymo2")
gtf_v1 <- load_file(file_v1)
# Eliminate redundant exons
nonredundant_exons <- eliminate_redundant_elements(gtf_v1, element_type = "exon")

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