Preprocess input GRanges object for splicing event calculation

This function checks that the input is a valid GRanges object with required metadata columns, then adds a unique key, the number of exons per transcript, and an 'internal' flag for each exon.

Usage

preprocess(gr, coef_col, method_string = NULL, additional_columns = NULL)

Arguments

gr

A GRanges object with metadata columns: 'exon_rank', 'gene_id', 'tx_id', 'coef'.

coef_col

The name of the metadata column indicating upregulated (+1) and downregulated (-1) exons.

method_string

The Differential Transcript Usage (DTU) method used to obtain the coef_col, for annotation purposes (optional).

additional_columns

A character vector of metadata column names to record for downstream use. Stored in metadata(result)$additional_columns (optional).

Value

A GRanges object with added 'key', 'nexons', and 'internal' columns.

Examples

# create mock data and run preprocessing
gr <- create_mock_data(n_genes = 2, n_tx_per_gene = 4, n_exons_per_tx = 4) |>
  preprocess(coef_col = "estimate", method_string = "mock_method")