buildCDS: Reference-guided construction of CDS on GTF object

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

Reference-guided construction of CDS on GTF object

Description

'buildCDS()' is designed to construct CDS information on transcripts from query GTF object.

Usage

buildCDS(query, ref, fasta)

Arguments

query	GRanges object containing query GTF data.
ref	GRanges object containing reference GTF data.
fasta	BSgenome or Biostrings object containing genomic sequence

Details

The 'buildCDS()'function will first search for known reference mRNAs in 'query' and annotate its CDS information. For the remaining transcripts, 'buildCDS()' will search for a putative translation start site using a database of annotated ATG codons from 'ref'. Transcripts containing an open-reading frame will be assigned the newly-determined CDS information.

Value

GRanges object containing query exon entries and newly-constructed CDS information

Author(s)

Fursham Hamid

Examples

# Load genome and datasets
library(BSgenome.Mmusculus.UCSC.mm10)
data(matched_query_gtf, ref_gtf)

# Build CDS
buildCDS(matched_query_gtf, ref_gtf, Mmusculus)

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