getCDS: Retrieve CDS information from UCSC

In IsoformSwitchAnalyzeR: Identify, Annotate and Visualize Alternative Splicing and Isoform Switches with Functional Consequences from both short- and long-read 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 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)

IsoformSwitchAnalyzeR documentation built on Nov. 8, 2020, 5:36 p.m.