stat_summary: Generate Summary Statistics for Genomic Elements

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

Generate Summary Statistics for Genomic Elements

Description

Calculates descriptive summary statistics (mean, median, standard deviation, etc.) for the lengths of exons or introns, grouped by classification (e.g., first exon, inner intron).

Usage

stat_summary(input, type, verbose = TRUE)

Arguments

input	A data frame containing classified exons or introns. For exons, must include EXON_CLASSIFICATION. For introns, requires classification columns.
type	A character string specifying the element type. Valid options: "exon" or "intron".
verbose	A logical indicating whether to print progress messages. Defaults to TRUE.

Details

For exons, statistics are grouped by EXON_CLASSIFICATION. For introns, groups include first_intron, inner_intron, and splice site types (e.g., gc_intron).

Value

A data frame with summary statistics for each element group, including mean, median, standard deviation, standard error, quartiles, and sample size.

Examples

file_v1 <- system.file("extdata", "gencode.v1.example.gtf.gz", package = "GencoDymo2")
gtf_v1 <- load_file(file_v1)
# Exon statistics
exon_stats <- stat_summary(gtf_v1, type = "exon")

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