Extract UTR and codon features from a GTFParquet object

Functions to extract UTR (untranslated region) and codon features from a GTFParquet object. These features are stored in the features.parquet file generated by gtf_to_parquet.py.

Usage

utrs(x, type = "both", filter = NULL)

# S4 method for class 'GTFParquet'
utrs(x, type = c("both", "5prime", "3prime"), filter = NULL)

codons(x, type = "both", filter = NULL)

# S4 method for class 'GTFParquet'
codons(x, type = c("both", "start", "stop"), filter = NULL)

Arguments

x

A GTFParquet object.

type

For utrs: one of "both", "5prime", or "3prime". For codons: one of "both", "start", or "stop".

filter

Optional named list for filtering features.

Value

A GRanges object with metadata columns including feature_type, transcript_id, and gene_id.

Examples

if (FALSE) { # \dontrun{
gtf <- GTFParquet(system.file("gc49", package="lkparq"))

# 5' UTRs
utr5 <- utrs(gtf, type = "5prime")

# 3' UTRs
utr3 <- utrs(gtf, type = "3prime")

# Start codons
start <- codons(gtf, type = "start")

# Stop codons
stop <- codons(gtf, type = "stop")
} # }