Retrieve CDS information from a selected repository from UCSC genome browser repositories.
A character, giving the genome. Currently supported are "hg19" and "mm9".
A character, giving the gene model repository. Currently supported are "ensemble", "UCSC" (knownGene), and "refseq".
For other genomes and/or gene model repositories, please construct a
CDSSet directly (see
For a full example of how to use
getCDS in a workflow, please see
CDSSet containing the annotated CDSs. For a description of the data.frame, see
Kristoffer Vitting-Seerup, Johannes Waage
Vitting-Seerup K, et al: spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data. BMC Bioinformatics 2014, 15:81.
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## Not run: mm9UCSC <- getCDS("mm9", "UCSC") ## End(Not run)
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