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Prepare exon ranges from a TxDb and DTU results table

Source: R/input_formatting.R
prepare_exons.Rd

Extracts exon ranges from a TxDb object, merges them with differential transcript usage (DTU) results, and returns a flat GRanges ready for preprocess.

Usage

prepare_exons(
  txdb,
  dtu_table,
  coef_col,
  tx_id_col = "tx_id",
  gene_id_col = "gene_id",
  verbose = TRUE
)

Arguments

txdb

A TxDb object (from GenomicFeatures).

dtu_table

A data.frame or tibble with DTU results. Must contain columns for transcript ID, gene ID, and a coefficient.

coef_col

Column name in dtu_table with the coefficient / effect size values.

tx_id_col

Column name in dtu_table with transcript IDs matching the TxDb transcript names. Default "tx_id".

gene_id_col

Column name in dtu_table with gene IDs. Default "gene_id".

verbose

Whether to print progress messages. Default TRUE.

Value

A GRanges object with metadata columns: gene_id, tx_id, exon_rank, the coefficient column, and any additional columns from dtu_table.