Generate Summary Statistics for Genomic Elements

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.

Value

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

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).

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")
#> Classifying exons...
#> Exon classification completed.
#> Calculating summary statistics...
#> Summary statistics calculation completed.