getCDS {IsoformSwitchAnalyzeR} | R Documentation |
Retrieve CDS information from a selected repository from UCSC genome browser repositories.
getCDS(selectedGenome, repoName)
selectedGenome |
A character, giving the genome. Currently supported are "hg19" and "mm9". |
repoName |
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 CDSSet
).
For a full example of how to use getCDS
in a workflow, please see analyzeORF
.
A CDSSet
containing the annotated CDSs. For a description of the dataframe, see CDSSet
.
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.
## Not run: mm9UCSC <- getCDS("mm9", "UCSC") ## End(Not run)