API for lenz99-/svmod
Calling somatic SVs in exome DNA-sequencing data (SV2 version)

Global functions
SV Source code
abbrevSeq Source code
addStatusForFLT3ITD Source code
addStatusToTestFromSim Source code
appendFiles Source code
applyOneClassSVM Source code
assessClippedBasesInRegion Source code
bamReadToClipPos Source code
checkTunedLearners Source code
cigarToPos Source code
cleanVirtualPatientData Source code
createPatient Source code
doMapping Source code
drawSamples Source code
estimateNGSPropFromMapping Source code
evalLearners2 Source code
evalLearners_OLD Source code
evalScreen Source code
evalTunedLearners Source code
evalTunedLearnersLoop Source code
evaluateOneClassSVM Source code
exploreClipping_BAM Source code
exploreClipping_G Source code
exploreGenomeVariants Source code
findClippedPeaks Source code
findClippedPeaks_G_OLD Source code
findCoveredRegionsInTarget Source code
findFeatureRegion Source code
findIntervals Source code
findIntervalsInCandidateRegions Source code
findIntervalsWrapper Source code
generatePatientReadStore Source code
getAffectedRange Source code
getChrom Source code
getClippedBasePositions Source code
getContextSeq Source code
getFeatureDataFromPatient Source code
getFeaturesFromMapping Source code
getFeaturesFromMappings Source code
getHammingWindowWeights Source code
getISDistForBWA Source code
getLength Source code
getLocus Source code
getNumberOfLinesUsingWC Source code
getPatNbr Source code
getPatStr Source code
getPatientIds Source code
getPatientMappingInfo Source code
getPosL Source code
getReadCountsFromMapping Source code
getSVSeq Source code
getShortName Source code
getTargetRegions Source code
getVirtualPatientFeatures Source code
getVirtualPatientPath Source code
harvestFeatures Source code
harvestLearnerPerformanceEvaluations_OLD Source code
harvestPerformanceEvaluations Source code
injectMySVs Source code
injectRandomSNVs Source code
injectSVInMapping Source code
lineCount Source code
localMax Source code
lookAtFeatureData Source code
makeLearnerList Source code
makeRLearner.classif.mcsvm2 Source code
makeRLearner.classif.ocsvm2 Source code
mapWrapper Source code
ngs.prop Source code
ocSVMTune Source code
onLoad Source code
onUnload Source code
parseNGSProp Source code
parseSampleProp Source code
plotLearnerPerformance Source code
plotScreenPerformance Source code
predictLearner.classif.mcsvm2 Source code
predictLearner.classif.ocsvm2 Source code
prepareFeatureData Source code
print.SV Source code
print.ngs.prop Source code
print.sample.prop Source code
processVirtualPatients Source code
rcpp_hello_world Source code
readSimulatorWrapper Source code
sample.prop Source code
setupParallel Source code
subSampleFastq Source code
subsampleInd Source code
toString.SV Source code
toString.ngs.prop Source code
toString.sample.prop Source code
trainLearner.classif.mcsvm2 Source code
trainLearner.classif.ocsvm2 Source code
tune_commented Source code
lenz99-/svmod documentation built on May 21, 2017, 11:40 a.m.