getCDS: Retrieve CDS information from UCSC

Description Usage Arguments Details Value Author(s) References Examples

View source: R/analyze_ORF.R

Description

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

Usage

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    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

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

kvittingseerup/IsoformSwitchAnalyzeR documentation built on May 12, 2021, 12:25 p.m.