Calculate GC Content of Genomic Features — calculate_gc

Computes the GC content percentage for exons or introns using genome sequence data from a BSgenome object.

Usage

calculate_gc_content(input, genome, verbose = TRUE)

Arguments

input: A data frame containing genomic features (exons/introns) with seqnames, start, end, and strand columns.
genome: A BSgenome object representing the reference genome (e.g., BSgenome.Hsapiens.UCSC.hg38).
verbose: A logical indicating whether to print progress messages. Defaults to TRUE.

Value

The input data frame with an additional gc_content column containing GC percentages for each feature.

Details

This function extracts the DNA sequence for each feature using genomic coordinates, then calculates the proportion of G and C nucleotides. Requires a BSgenome package for the relevant genome.

Examples

library(BSgenome.Hsapiens.UCSC.hg38)
file_v1 <- system.file("extdata", "gencode.v1.example.gtf.gz", package = "GencoDymo2")
gtf_v1 <- load_file(file_v1)
gtf_with_gc <- calculate_gc_content(gtf_v1, genome = BSgenome.Hsapiens.UCSC.hg38, verbose = FALSE)