Identify Single-Exon Genes/Transcripts in GENCODE Data

This function identifies single-exon genes or transcripts from a genomic annotation dataset, typically obtained from the GENCODE database. It processes input data, either from a file or an already loaded data frame, and returns either single-exon genes or single-exon transcripts based on the user's selection. The function works seamlessly with GTF/GFF files or data frames that include the standard GENCODE annotation fields. This is especially useful for identifying genes or transcripts that do not undergo splicing.

Usage

extract_single_exon(input, level = "gene", output_file = NULL)

Arguments

input

Either a file path to a GTF/GFF3 file or a data frame representing genomic annotations. The input data should contain at least the columns type, gene_id, transcript_id, and exon_number. If a file path is provided, it is assumed to be a GTF/GFF file.

level

A character string specifying the level of analysis. It should be either "gene" or "transcript". The default is "gene". The selection allows users to specify whether they want to identify single-exon genes or single-exon transcripts in the annotation.

output_file

Optional. A file path to save the results as a tab-separated file. If not provided, the results will not be saved. The file will include the IDs of the single-exon genes or transcripts along with their respective exon IDs. This feature is useful for exporting results for further analysis or reporting purposes.

Value

A data frame containing the IDs of single-exon genes or transcripts based on the selected level. The returned data frame contains the following columns:

• gene_id or transcript_id: The IDs of the single-exon genes or transcripts.

• exon_count: The count of exons for each entity (always 1 for single-exon entities).

• exon_id: The ID of the exon associated with the single-exon gene or transcript.

The data frame can then be used for downstream analysis, such as identifying unique single-exon genes or transcripts, or for exporting to a file.

Details

1. Input Validation: Checks for required columns and valid level specification.

2. Exon Counting: Groups exons by gene/transcript and counts occurrences.

3. Single-Exon Filtering: Retains only entities with exactly one exon.

4. Output: Returns filtered results; optionally writes to file.

See also

extract_introns, load_file

Examples

# Example input data frame
input <- data.frame(
  type = c("exon", "exon", "exon", "exon", "exon"),
  gene_id = c("gene1", "gene1", "gene2", "gene3", "gene4"),
  transcript_id = c("tx1", "tx1", "tx2", "tx3", "tx4"),
  exon_number = c(1, 2, 1, 1, 1),
  exon_id = c("e1", "e2", "e1", "e1", "e1")
)

# Identify single-exon genes
single_exon_genes <- extract_single_exon(input, level = "gene")
print(single_exon_genes)
#>   gene_id exon_count exon_id
#> 1   gene2          1      e1
#> 2   gene3          1      e1
#> 3   gene4          1      e1

# Identify single-exon transcripts
single_exon_transcripts <- extract_single_exon(input, level = "transcript")
print(single_exon_transcripts)
#>   transcript_id exon_count exon_id
#> 1           tx2          1      e1
#> 2           tx3          1      e1
#> 3           tx4          1      e1