compare_release: Compare Annotation Counts Between Two GENCODE Releases

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

Compare Annotation Counts Between Two GENCODE Releases

Description

Compares the number of annotated genomic elements (genes, transcripts, exons, introns) between two specified GENCODE releases. The function accepts input data as either file paths (in GTF/GFF format) or pre-loaded data frames. It computes the absolute difference (delta), the percentage change relative to a chosen baseline, and determines the direction of change (increase or decrease).

Usage

compare_release(input1, input2, type, gene_type = NULL, baseline = "count2")

Arguments

input1	A character string specifying the file path to a GTF/GFF file from the first GENCODE release, or a data frame containing the annotation data.
input2	A character string specifying the file path to a GTF/GFF file from the second GENCODE release, or a data frame containing the annotation data.
type	A character string indicating the type of genomic element to compare. Valid options are "gene", "transcript", "exon", or "intron".
gene_type	An optional character string specifying a particular gene biotype to filter comparisons (e.g., "protein_coding", "lncRNA"). If NULL (default), all gene types are included.
baseline	A character string defining the baseline for calculating percentage change. Options include: "count1": Uses the count from the first input (release) as the baseline. "count2": Uses the count from the second input (release) as the baseline (default). "average": Uses the average of the counts from both inputs as the baseline.

Details

This function processes two GENCODE releases to compare annotation counts for a specified genomic element type. Key steps include:

1. Input Handling: If inputs are file paths, they are loaded into data frames using the load_file function. Data frames are used directly.

2. Element Filtering: If gene_type is specified, annotations are filtered to include only that gene biotype.

3. Count Calculation: The number of elements (genes, transcripts, etc.) of the specified type is counted in each release.

4. Delta and Percentage: The absolute difference (delta) and percentage change are calculated based on the chosen baseline.

5. Direction Determination: The direction of change is determined by comparing counts between the two releases.

The function provides both numerical results and a formatted console output highlighting key metrics.

Value

A list with the following elements:

• delta: The absolute difference in the number of annotations.

• percentage: The percentage change relative to the selected baseline.

• direction: A string indicating the direction of the change ("increase", "decrease", or "no change").

See Also

load_file, get_gtf, get_gff3.

Examples

file_v1 <- system.file("extdata", "gencode.v1.example.gtf.gz", package = "GencoDymo2")
file_v2 <- system.file("extdata", "gencode.v2.example.gtf.gz", package = "GencoDymo2")
# Example 1: Using data frames with the provided example GTF files
gtf_v1 <- load_file(file_v1)
gtf_v2 <- load_file(file_v2)
comparison <- compare_release(gtf_v1, gtf_v2, type = "gene")

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