make_eventdata_plus: make_eventdata_plus

In splikit: Analysing RNA Splicing in Single-Cell RNA Sequencing Data

make_eventdata_plus

Description

This function reads in a GTF file, extracts gene annotations, and merges them with event-level genomic intervals provided by the user. The final data table contains the original event intervals and the corresponding gene information (for example, gene_id and gene_name).

Usage

make_eventdata_plus(eventdata, GTF_file_direction)

Arguments

eventdata	A data table of genomic intervals for events. Must contain columns: chr: Chromosome name (e.g., "chr1"). start: Start coordinate of the event. end: End coordinate of the event. strand: Numeric strand indicator (1 or 2).
GTF_file_direction	A character string specifying the path to a GTF file. The file must contain at least these columns: seqid, start, end, strand, gene_id, and gene_name.

Details

1. Read the GTF: Uses data.table::fread to load GTF data and convert it to a data table.

2. Subset for Genes: Keeps only rows where type == "gene", retaining columns for chromosome, start, end, strand, gene_id, and gene_name.

3. Strand Conversion: Merges the GTF data with a small lookup table to replace + and - with numeric strand indicators 1 and 2 (matching STAR).

4. Overlaps: With both data sets keyed, uses foverlaps() from data.table to find intervals in eventdata that fall fully within gene boundaries.

Value

A data table containing overlapping event intervals with added gene metadata (such as gene_id and gene_name). The columns returned will include both event-level and gene-level information.

splikit documentation built on May 13, 2026, 9:08 a.m.