getCDS {IsoformSwitchAnalyzeR} | R Documentation

## Retrieve CDS information from UCSC

### Description

Retrieve CDS information from a selected repository from UCSC genome browser repositories.

### Usage

        getCDS(selectedGenome, repoName)

### Arguments

`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".

### Details

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`.

### Value

A `CDSSet` containing the annotated CDSs. For a description of the data.frame, see `CDSSet`.

### Author(s)

Kristoffer Vitting-Seerup, Johannes Waage

### References

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.

### Examples

        ## Not run:
            mm9UCSC <- getCDS("mm9", "UCSC")

    ## End(Not run)

[Package IsoformSwitchAnalyzeR version 1.14.1 Index]