spliced_trans_length: Calculate Spliced Transcript Lengths

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

Calculate Spliced Transcript Lengths

Description

Computes the spliced length of transcripts by summing the lengths of their constituent exons. This represents the mature RNA length after intron removal.

Usage

spliced_trans_length(input)

Arguments

input

A data frame containing GENCODE annotations in GTF format, including type, transcript_id, and width columns.

Details

This function processes the input data to:

1. Filter entries to include only exons.

2. Group exons by transcript ID.

3. Sum the widths of all exons per transcript.

The result provides the total length of the mature spliced RNA for each transcript.

Value

A data frame with two columns: transcript_id and transcript_length, where the latter is the sum of exon widths for each transcript.

Examples

file_v1 <- system.file("extdata", "gencode.v1.example.gtf.gz", package = "GencoDymo2")
gtf_v1 <- load_file(file_v1)
spliced_lengths <- spliced_trans_length(gtf_v1)

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