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  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2013-12-28 17:17:25 UTC
  • mfrom: (1.1.2)
  • Revision ID: package-import@ubuntu.com-20131228171725-polmzo8go4m371c6
Tags: 2.4.1-1
* New upstream version
* debian/rules: Remove useless creation of ${R-Depends}
* debian/control: Versioned Build-Depends: r-base-dev (>= 3.0)
* debian/README.test: add hint how to test the package

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R/AllClasses.R
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#TODO: I get the distinct feeling that these two should be nested environments, but I don't really know what that means.
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#CuffRun class describes information about a Cuffdiff run?
 
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#setClass("CuffRun",
 
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#               representation(DB = "SQLiteConnection",
 
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#                                               sampleInfo = "data.frame",
 
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#                                               runParams = "data.frame"
 
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#                                               )
 
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#               )
 
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#CuffData Class is a 'pointer' container to a group of features in a cufflinks dataset
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setClass("CuffData",
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                representation(DB = "SQLiteConnection",
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#CuffSet Class is a 'pointer' container to a group of CuffData elements in a cufflinks dataset
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setClass("CuffSet",
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                representation(DB = "SQLiteConnection",
 
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                                                runInfo = "data.frame",
 
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                                                phenoData = "data.frame",
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                                                conditions = "data.frame",
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                                                genes = "CuffData",
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                                                isoforms = "CuffData",
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setClass("CuffFeature",
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                representation(annotation="data.frame",
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                                                fpkm="data.frame",
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                                                diff="data.frame"
 
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                                                diff="data.frame",
 
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                                                repFpkm="data.frame",
 
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                                                count="data.frame",
 
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                                                genome="character"
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                                )
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                )
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#CuffGene is a 'data' container for all information linked to a single 'gene_id'
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setClass("CuffGene",
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                representation(id = "character",
 
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                                                features = "data.frame",
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                                                isoforms = "CuffFeature",
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                                                TSS = "CuffFeature",
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                                                CDS = "CuffFeature",
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setClass("CuffFeatureSet",
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                representation(annotation="data.frame",
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                                fpkm="data.frame",
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                                diff="data.frame"
 
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                                diff="data.frame",
 
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                                repFpkm="data.frame",
 
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                                count="data.frame",
 
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                                genome="character"
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                        )
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)
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