getCDS: Retrieve CDS information from UCSC

In spliceR: Classification of alternative splicing and prediction of coding potential from RNA-seq data.

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 annotatePTC.

Value

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

Author(s)

Kristoffer Vitting-Seerup, Johannes Waage

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)

spliceR documentation built on May 2, 2018, 2:50 a.m.