A container for coding sequence annotation information.
This object can be generated automatically from
getCDS, or can be be generated manually by creating a new CDSSet from a data.frame with the following columns:
chrom, the chromosome name (NB: chromosome names must match when running
strand, the strand,
cdsStart, the genomic start of the coding sequence (beware of 0/1-frame issuses), and
cdsEnd, the genomic end of the coding sequence (beware of 0/1-frame issuses).
CDSset object is required by
annotatePTC for translation of transcripts and premature termination codon annotation.
For an example, see
Kristoffer Vitting-Seerup, Johannes Waage
Vitting-Seerup K , Porse BT, Sandelin A, Waage J. (2014) spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 15:81.
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