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Compare Annotation Counts Between Two GENCODE Releases

Source: R/utils.R
compare_release.Rd

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.

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").

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.

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")
#> Delta: 1
#> Percentage: 33.333%
#> Change Direction: increase