matchGeneInfo: Match gene metadata from query GTF to a reference GTF

In fursham-h/factR: Functional Annotation of Custom Transcriptomes

Match gene metadata from query GTF to a reference GTF

Description

'matchGeneInfo()' matches and corrects Gene IDs from a query GTF object to a reference GTF

Usage

matchGeneInfo(query, ref, primary_gene_id = NULL, secondary_gene_id = NULL)

Arguments

query	Query GTF imported as GRanges object
ref	Reference GTF as GRanges object
primary_gene_id	Character name of the primary gene id metadata in query GTF. Input to this argument is typically 'gene_id'
secondary_gene_id	Character name of the secondary gene id in query file. Example of input to this argument is 'ref_gene_id'

Details

The default approach to this correction relies on finding overlaps between transcripts in query with transcripts in reference. Using this method alone could result in false positive matches (19 percent false positives). To improve this, users have the option to invoke two additional layers of matching. (1) Matching by ENSEMBL Gene_IDs. If both query and reference transcript annotations containg Ensembl-style Gene IDs, this program will try to match both IDs in a less stringent manner. This correction can be invoked by providing the 'primary_gene_id' argument

(2) Matching by secondary Gene_IDs. Depending on the transcript assembly program, GTF/GFF3 annotations may contain additional comments on the transcript information. This may include a distinct secondary Gene ID annotation that potentially matches with the reference. To invoke this correction, provide 'primary_gene_id' and 'secondary_gene_id' arguments. To determine if your transcript assembly contain possible secondary Gene IDs, import query GTF file using 'importGTF()' and check its metadata columns

Value

Gene_id-matched query GRanges

Author(s)

Fursham Hamid

Examples

## ---------------------------------------------------------------------
## EXAMPLE USING SAMPLE DATASET
## ---------------------------------------------------------------------
# Load datasets
data(chrom_matched_query_gtf, ref_gtf)

# Run matching function
matchGeneInfo(chrom_matched_query_gtf, ref_gtf)

fursham-h/factR documentation built on Aug. 20, 2023, 1:58 p.m.