buildCDS.RdConstructs CDS information on transcripts from custom annotation using reference-based approach.
buildCDS(object, verbose = FALSE)factRObject
Whether to print out messages (Default: FALSE)
Updated factRObject. The GTF GenomicRanges object will now contain "CDS" type features.
The `cds` variable from the transcript metadata will return "yes" for coding transcripts and "no" for non-coding transcripts
This function will firstly identify custom transcripts with identical exon structures as those in the reference annotation. If these reference transripts contain CDS segments, the coordinates will be passed to its paired- custom transcript. The putative start codon of the remaining transcripts will be the first ATG sequence that is in-frame with the coding sequence of reference transcripts and an in-frame stop codon will be determined.
## Load sample data
data(factRsample)
## Build coding sequences
factRsample <- buildCDS(factRsample)