spliceR (version 1.14.0)

getCDS: 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".

Value

A CDSSet containing the annotated CDSs. For a description of the dataframe, see CDSSet.

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 annotatePTC.

References

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.

Examples

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