subsetNewTranscripts: Shortlist GTF GRanges object for new transcripts

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

Shortlist GTF GRanges object for new transcripts

Description

'subsetNewTranscripts()' will retain transcripts in 'query' that are distinct from those in 'ref'

Usage

subsetNewTranscripts(query, ref, refine.by = c("none", "intron", "cds"))

Arguments

query	GRanges object containing query GTF data.
ref	GRanges object containing reference GTF data.
refine.by	Whether to refine the selection process by removing query transcripts with similar introns or CDS structure to reference. Default input is "none", and can be changed to "intron" or "cds" respectively.

Details

'subsetNewTranscripts()' will compare query and reference GTF GRanges and return query transcripts with different exon structures from reference transcripts. Transcriptome assemblers may sometime extend 5' and 3' ends of known transcripts based on experimental data. These annotated transcripts can be removed by inputting "intron" to the refine.by argument. This will further compare and remove transcripts of identical intron structures. Alternatively, transcripts with unique CDS coordinates can be selected by typing "cds" to the refine.by argument.

Value

Filtered GRanges GTF object

Author(s)

Fursham Hamid

Examples

# Load dataset
data(matched_query_gtf, ref_gtf)

# shortlist new transcripts
subsetNewTranscripts(matched_query_gtf, ref_gtf)

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