#TCGAGeneReport 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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# internal
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getMirs_List_internal <- function(theZipFile, theMethodString, theVerboseFlag)
{
setJavaVerboseFlag(theVerboseFlag)
results <- NULL
jListGenesObj <- .jnew("org/mda/bcb/tcgagsdata/CallFromR", theZipFile)
results <- .jcall(jListGenesObj, returnSig = "[S", method=theMethodString)
results
}
getMirs_Metadata_internal <- function(theId, theZipFile, theMethodString, theVerboseFlag)
{
setJavaVerboseFlag(theVerboseFlag)
result <- NULL
jReadGeneObj <- .jnew("org/mda/bcb/tcgagsdata/CallFromR", theZipFile)
jObj <- .jcall(jReadGeneObj,
returnSig = "[Lorg/mda/bcb/tcgagsdata/retrieve/MetadataMir;",
method=theMethodString,
.jnew("java/lang/String",theId))
if(FALSE==is.jnull(jObj))
{
{
result <- as.vector(unlist(lapply(jObj, function(theObj)
{
new("Metadata_Mir",
theMirId=theObj$mMirId,
theMimatId=theObj$mMimatId,
theMirType=theObj$mMirType,
theChromosome=theObj$mChromosome,
theLocationStart=theObj$mLocationStart,
theLocationEnd=theObj$mLocationEnd,
theStrand=theObj$mStrand,
theDerivedFrom=theObj$mDerivedFrom)
})))
}
}
result
}
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# exported
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####
#### uses mirs from data file
####
getMirs_List_Mir <- function(theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", theVerboseFlag=FALSE)
{
getMirs_List_internal(theZipFile, 'getMirList', theVerboseFlag=theVerboseFlag)
}
getMirs_List_Mimat <- function(theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", theVerboseFlag=FALSE)
{
getMirs_List_internal(theZipFile, 'getMimatList', theVerboseFlag=theVerboseFlag)
}
getMirs_Metadata_Mir <- function(theMirId, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", theVerboseFlag=FALSE)
{
getMirs_Metadata_internal(theMirId, theZipFile, 'getMetadata_miRNA_mir', theVerboseFlag=theVerboseFlag)
}
getMirs_Metadata_Mimat <- function(theMimatId, theZipFile="/rsrch1/bcb/batcheffects/GENE_REPORT/GeneSurvey.zip", theVerboseFlag=FALSE)
{
getMirs_Metadata_internal(theMimatId, theZipFile, 'getMetadata_miRNA_mimat', theVerboseFlag=theVerboseFlag)
}
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