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Extract Transcript-to-Gene Mapping from GFF3 File

Source: R/build_se.R
extract_tx2gene_from_gff3.Rd

Internal function that parses GFF3 or GFF3.gz files to extract transcript-to-gene mappings. This function is called internally by build_se() when a GFF3 file path is provided. Users should not call this function directly.

Usage

extract_tx2gene_from_gff3(gff3_file)

Arguments

gff3_file

Path to a GFF3 or GFF3.gz file containing transcript/mRNA features with ID and Parent attributes.

Value

A data.frame with two columns (Transcript, Gene) containing the transcript-to-gene mapping extracted from the GFF3 file.

Details

The function expects GFF3 format with the following structure:

  • 9 tab-separated columns: seqname, source, feature, start, end, score, strand, phase, attributes

  • Feature type column (3rd column) should contain 'transcript' or 'mRNA'

  • Attributes column (9th column) should contain ID and Parent fields

  • ID field: unique identifier for the transcript

  • Parent field: references the gene ID that this transcript belongs to

Example GFF3 line:

chr1\tgencode\ttranscript\t1000\t3000\t.\t+\t.\t
ID=ENST00000001;Parent=ENSG00000101;Name=BRCA1-001

Performance: This function is optimized for large GFF3 files:

  • Reads files in 10,000-line chunks (not line-by-line)

  • Uses fast pre-filtering (feature type check before regex)

  • Employs efficient string operations instead of heavy regex on every line

  • Handles both compressed (.gz) and uncompressed files seamlessly

Examples

if (FALSE) { # \dontrun{
# Create a temporary GFF3 file with transcript features
gff3_lines <- c(
  'chr1\tgencode\ttranscript\t1000\t3000\t.\t+\t.\tID=ENST001;Parent=ENSG001',
  'chr1\tgencode\ttranscript\t1500\t3500\t.\t+\t.\tID=ENST002;Parent=ENSG001',
  'chr2\tgencode\ttranscript\t5000\t8000\t.\t-\t.\tID=ENST003;Parent=ENSG002'
)
tf <- tempfile(fileext = '.gff3')
writeLines(gff3_lines, tf)

# Extract transcript-to-gene mapping
tx2gene <- extract_tx2gene_from_gff3(tf)
head(tx2gene)
} # }