Files in oyvble/MPSproto
A Quantitative Model for MPS data with complex stutters
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md
R/calcLogLikC_prediction.R
R/calcLogLikR_prediction.R
R/calibrateModel.R
R/convertBracket2seq.R
R/convertMotifReps2seq.R
R/createDiagnosticPlots.R
R/deconvolve.R
R/diagnoseMCMC.R
R/doMCMC.R
R/dpareto.R
R/fitSUMmodel.R
R/genMPSevidence.R
R/getMPSkit.R
R/getMarkerEffStat.R
R/getMotifReps.R
R/getMotifRepsSequences.R
R/getResults.R
R/getStutterData.R
R/getStutterExpectations.R
R/getStutterIndex.R
R/getStutterTypeRule.R
R/getStutteredSequence.R
R/getUpperLR.R
R/gui.R
R/importMPSfreqs.R
R/importMPSsample.R
R/inferEvidence.R
R/inferEvidence2.R
R/inferMarkerEfficiency.R
R/inferNoiseModel.R
R/inferStutterModel.R
R/insertMissingTrueAlleles.R
R/logLiki.R
R/optimizeLik.R
R/plotMPS.R
R/plotTopMPS.R
R/prefit_prediction.R
R/prepareC_prediction.R
R/prepareData_prediction.R
R/sample_listToTable.R
R/tableReader.R
R/validMLE.R
README.md
doc/MPSproto_MathematicalDetails.docx
doc/MPSproto_tutorial.Rmd
doc/MPSproto_tutorial.html
doc/MPSproto_tutorial_advanced.Rmd
doc/MPSproto_tutorial_advanced.html
doc/tutorialDataCalibrated.RDS
inst/MPSproto_stutterCharPaper/README.txt
inst/MPSproto_stutterCharPaper/calibrate.R
inst/MPSproto_stutterCharPaper/data/ForenSeq_Norway_FWbrack.csv
inst/MPSproto_stutterCharPaper/data/calibrated_MPSproto_stutterCharPaper.RDS
inst/MPSproto_stutterCharPaper/data/calibrated_StutterCoef.csv
inst/MPSproto_stutterCharPaper/data/data_excludedStutters.csv
inst/MPSproto_stutterCharPaper/data/data_noise.csv
inst/MPSproto_stutterCharPaper/data/data_sumPerMarker.csv
inst/MPSproto_stutterCharPaper/interpret.R
inst/examples/ForenSeq_NIST1036cauc_FWbrack.csv
inst/examples/MPS_evid2p.csv
inst/examples/MPS_evid2p_CE.csv
inst/examples/MPS_evid2p_missing.csv
inst/examples/MPS_evid2p_missing2.csv
inst/examples/MPS_evid2p_refs.csv
inst/examples/MPS_evid2p_refsMissing.csv
inst/examples/proj.Rdata
inst/examples/tutorialDataCalibrated.RDS
inst/examples/tutorialDataCalibration.RDS
inst/examples/tutorialData_preparedCobj.RDS
inst/extdata/BLMM_CE_table.txt
inst/extdata/kit.txt
inst/extdata/kit_mps.txt
man/calcLogLikC_prediction.Rd
man/calcLogLikR_prediction.Rd
man/calibrateModel.Rd
man/convertBracket2seq.Rd
man/convertMotifReps2seq.Rd
man/createDiagnosticPlots.Rd
man/deconvolve.Rd
man/diagnoseMCMC.Rd
man/doMCMC.Rd
man/dpareto.Rd
man/fitSUMmodel.Rd
man/genMPSevidence.Rd
man/getMPSkit.Rd
man/getMarkerEffStat.Rd
man/getMotifReps.Rd
man/getMotifRepsSequences.Rd
man/getStutterData.Rd
man/getStutterExpectations.Rd
man/getStutterIndex.Rd
man/getStutterTypeRule.Rd
man/getStutteredSequence.Rd
man/getUpperLR.Rd
man/gui.Rd
man/importMPSfreqs.Rd
man/importMPSsample.Rd
man/inferEvidence.Rd
man/inferEvidence2.Rd
man/inferMarkerEfficiency.Rd
man/inferNoiseModel.Rd
man/inferStutterModel.Rd
man/insertMissingTrueAlleles.Rd
man/logLiki.Rd
man/optimizeLik.Rd
man/plotMPS.Rd
man/plotTopMPS.Rd
man/prefit_prediction.Rd
man/prepareC_prediction.Rd
man/prepareData_prediction.Rd
man/sample_listToTable.Rd
man/tableReader.Rd
man/validMLE.Rd
src/Makevars
src/Makevars.win
src/loglikPrediction_allcomb.cpp
src/loglikPrediction_allcomb2.cpp
src/loglikPrediction_cumprob.cpp
tests/testthat.R
tests/testthat/test_getStutterIndex.R
tests/testthat/test_interpretations_nodeg.R
tests/testthat/test_interpretations_nodeg_missing.R
tests/testthat/test_interpretations_withdeg.R
tests/testthat/test_loglikPrediction_allcomb.R
