Read in a GTF file and convert to GenomicRanges or data.table

Read in a GTF file, such as one from Ensembl, and convert it to a GenomicRanges object or data.table with refactored seq details. The GTF file can be either zipped or unzipped. Supports filtering by feature type and additional GTF-specific processing.

Usage

read_gtf_file(
  gtf_file,
  output_type = c("gr", "dt"),
  feature_type = NULL,
  gene_biotype = NULL,
  seq_lengths = gUtils::hg_seqlengths(),
  verbose = TRUE
)

Arguments

gtf_file

Path to GTF file (supports .gtf, .gtf.gz)

output_type

Character string specifying output format: gr="GenomicRanges" (default) or dt="data.table"

feature_type

Character vector of feature types to retain (e.g., "gene", "transcript", "exon", "CDS"). If NULL, all features are retained. Default: NULL

gene_biotype

Character vector of gene biotypes to retain (e.g., "protein_coding", "lncRNA"). If NULL, all biotypes are retained. Default: NULL

seq_lengths

Named vector object used as template for new seq details. See gUtils::hg_seqlengths() for example. Default: hg38 seqlengths. Only used when output_type = "GenomicRanges"

verbose

Logical, whether to print progress messages. Default: TRUE

Value

GenomicRanges object or data.table with GTF data and updated seqinfo