#GeneSurvey Copyright 2014, 2015, 2016 University of Texas MD Anderson Cancer Center
#
#This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 2 of the License, or (at your option) any later version.
#
#This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
#
#You should have received a copy of the GNU General Public License along with this program. If not, see <http://www.gnu.org/licenses/>.
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.onAttach <- function(libname, pkgname)
{
packageStartupMessage(paste(geneReportVersion()))
}
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setClass("Metadata_Mir", representation(
mMirId="character",
mMimatId="character",
mMirType="character",
mChromosome="character",
mLocationStart="numeric",
mLocationEnd="numeric",
mStrand="character",
mDerivedFrom="character"))
setMethod("initialize", "Metadata_Mir",
function(.Object,
theMirId,
theMimatId,
theMirType,
theChromosome,
theLocationStart,
theLocationEnd,
theStrand,
theDerivedFrom)
{
.Object@mMirId <- theMirId
.Object@mMimatId <- theMimatId
.Object@mMirType <- theMirType
.Object@mChromosome <- theChromosome
.Object@mLocationStart <- theLocationStart
.Object@mLocationEnd <- theLocationEnd
.Object@mStrand <- theStrand
.Object@mDerivedFrom <- theDerivedFrom
.Object
})
setGeneric(name="get.MirId", def=function(theObject){standardGeneric("get.MirId")})
setMethod(f="get.MirId",
definition=function(theObject)
{
theObject@mMirId
})
setGeneric(name="get.MimatId", def=function(theObject){standardGeneric("get.MimatId")})
setMethod(f="get.MimatId",
definition=function(theObject)
{
theObject@mMimatId
})
setGeneric(name="get.MirType", def=function(theObject){standardGeneric("get.MirType")})
setMethod(f="get.MirType",
definition=function(theObject)
{
theObject@mMirType
})
setGeneric(name="get.LocationStart", def=function(theObject){standardGeneric("get.LocationStart")})
setMethod(f="get.LocationStart",
definition=function(theObject)
{
theObject@mLocationStart
})
setGeneric(name="get.LocationEnd", def=function(theObject){standardGeneric("get.LocationEnd")})
setMethod(f="get.LocationEnd",
definition=function(theObject)
{
theObject@mLocationEnd
})
setGeneric(name="get.Chromosome", def=function(theObject){standardGeneric("get.Chromosome")})
setMethod(f="get.Chromosome",
definition=function(theObject)
{
theObject@mChromosome
})
setGeneric(name="get.Strand", def=function(theObject){standardGeneric("get.Strand")})
setMethod(f="get.Strand",
definition=function(theObject)
{
theObject@mStrand
})
setGeneric(name="get.DerivedFrom", def=function(theObject){standardGeneric("get.DerivedFrom")})
setMethod(f="get.DerivedFrom",
definition=function(theObject)
{
theObject@mDerivedFrom
})
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setClass("Metadata_Gene", representation(
mGeneSymbol="character",
mGeneId="character",
mVersionIndex="character",
mChromosome="character",
mLocationStart="numeric",
mLocationEnd="numeric",
mStrand="character"))
setMethod("initialize", "Metadata_Gene",
function(.Object,
theGeneSymbol,
theGeneId,
theVersionIndex,
theChromosome,
theLocationStart,
theLocationEnd,
theStrand)
{
.Object@mGeneSymbol <- theGeneSymbol
.Object@mGeneId <- theGeneId
.Object@mVersionIndex <- theVersionIndex
.Object@mChromosome <- theChromosome
.Object@mLocationStart <- theLocationStart
.Object@mLocationEnd <- theLocationEnd
.Object@mStrand <- theStrand
.Object
})
setGeneric(name="get.GeneSymbol", def=function(theObject){standardGeneric("get.GeneSymbol")})
setMethod(f="get.GeneSymbol",
definition=function(theObject)
{
theObject@mGeneSymbol
})
setGeneric(name="get.GeneId", def=function(theObject){standardGeneric("get.GeneId")})
setMethod(f="get.GeneId",
definition=function(theObject)
{
theObject@mGeneId
})
setGeneric(name="get.VersionIndex", def=function(theObject){standardGeneric("get.VersionIndex")})
setMethod(f="get.VersionIndex",
definition=function(theObject)
{
theObject@mVersionIndex
})
setGeneric(name="get.LocationStart", def=function(theObject){standardGeneric("get.LocationStart")})
setMethod(f="get.LocationStart",
definition=function(theObject)
{
theObject@mLocationStart
})
setGeneric(name="get.LocationEnd", def=function(theObject){standardGeneric("get.LocationEnd")})
setMethod(f="get.LocationEnd",
definition=function(theObject)
{
theObject@mLocationEnd
})
setGeneric(name="get.Chromosome", def=function(theObject){standardGeneric("get.Chromosome")})
setMethod(f="get.Chromosome",
definition=function(theObject)
{
theObject@mChromosome
})
setGeneric(name="get.Strand", def=function(theObject){standardGeneric("get.Strand")})
setMethod(f="get.Strand",
definition=function(theObject)
{
theObject@mStrand
})
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setClass("Metadata_Probe", representation(
mName="character",
mChromosome="character",
mProbeLocation="numeric",
mStrand="character",
mGeneStructure="vector"))
setMethod("initialize", "Metadata_Probe",
function(.Object,
theName,
theChromosome,
theProbeLocation,
theStrand,
theGeneStructure)
{
.Object@mName <- theName
.Object@mChromosome <- theChromosome
.Object@mProbeLocation <- theProbeLocation
.Object@mStrand <- theStrand
.Object@mGeneStructure <- theGeneStructure
.Object
})
setGeneric(name="get.Name", def=function(theObject){standardGeneric("get.Name")})
setMethod(f="get.Name",
definition=function(theObject)
{
theObject@mName
})
setGeneric(name="get.Chromosome", def=function(theObject){standardGeneric("get.Chromosome")})
setMethod(f="get.Chromosome",
definition=function(theObject)
{
theObject@mChromosome
})
setGeneric(name="get.ProbeLocation", def=function(theObject){standardGeneric("get.ProbeLocation")})
setMethod(f="get.ProbeLocation",
definition=function(theObject)
{
theObject@mProbeLocation
})
setGeneric(name="get.Strand", def=function(theObject){standardGeneric("get.Strand")})
setMethod(f="get.Strand",
definition=function(theObject)
{
theObject@mStrand
})
setGeneric(name="get.GeneStructure", def=function(theObject){standardGeneric("get.GeneStructure")})
setMethod(f="get.GeneStructure",
definition=function(theObject)
{
theObject@mGeneStructure
})
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# myMatrix <- matrix(data=c(0,0,0,0,20,0,0,0,30,10,0,0,10,10,20,0), byrow=TRUE, ncol=4, nrow=4, dimnames=list(c("Bob", "Ted", "Carol", "Alice"),c("Bob", "Ted", "Carol", "Alice")))
# new("ReadGene_Item", NULL, "foo", myMatrix, NULL)
#setClassUnion("VectorOrNULL", c("vector", "NULL"))
#setClassUnion("CharacterOrNULL", c("character", "NULL"))
#setClassUnion("ReadProbeOrNULL", c("ReadProbe", "NULL"))
#setClassUnion("ReadGenomeOrNULL", c("ReadGenome", "NULL"))
#setClassUnion("ReadGenomeOrNULL", c("NULL"))
# mData -- matrix samples in rows, probes in columns, with row and column names
setClass("GeneReportDataObject", representation(
mData="matrix",
mSampleAnnotations="data.frame",
mGenomeAnnotations="data.frame",
mTissueAnnotations="data.frame"))
setMethod("initialize", "GeneReportDataObject",
function(.Object,
theData,
theSampleAnnotations,
theGenomeAnnotations,
theTissueAnnotations)
{
.Object@mData <- theData
.Object@mSampleAnnotations <- theSampleAnnotations
.Object@mGenomeAnnotations <- theGenomeAnnotations
.Object@mTissueAnnotations <- theTissueAnnotations
.Object
})
setGeneric(name="get.Data", def=function(theObject){standardGeneric("get.Data")})
setMethod(f="get.Data",
definition=function(theObject)
{
theObject@mData
})
setGeneric(name="get.SampleAnnotations", def=function(theObject){standardGeneric("get.SampleAnnotations")})
setMethod(f="get.SampleAnnotations",
definition=function(theObject)
{
theObject@mSampleAnnotations
})
setGeneric(name="get.GenomeAnnotations", def=function(theObject){standardGeneric("get.GenomeAnnotations")})
setMethod(f="get.GenomeAnnotations",
definition=function(theObject)
{
theObject@mGenomeAnnotations
})
setGeneric(name="get.TissueAnnotations", def=function(theObject){standardGeneric("get.TissueAnnotations")})
setMethod(f="get.TissueAnnotations",
definition=function(theObject)
{
theObject@mTissueAnnotations
})
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