Files in jsemple19/EMclassifieR
Classify DSMF data using the Expectation Maximisation algorithm
.Rbuildignore
.gitignore
DESCRIPTION
EMclassifieR.Rproj
NAMESPACE
R/EMbasic.R
R/EMmultigene.R
R/classifyByKnownClasses.R
R/clusterUtils.R
R/doparImport.R
R/magitterImport.R
R/preProcessMethMats.R
R/utils.R
README.md
inst/extdata/EMres/allClassMeans_dS02-182_multiGene.rds
inst/extdata/EMres/dS02-182_multiGene_K4.rds
inst/extdata/EMres/dS02-182_multiGene_K5.rds
inst/extdata/EMres/dS02-182_multiGene_K6.rds
inst/extdata/csv/MatrixLog_relCoord_ampTSS.csv
inst/extdata/rds/allClassMeans_dS02-182_WBGene00015947.rds
inst/extdata/rds/ampliconMaxTSSgr.RDS
inst/extdata/rds/relCoord_ampTSS/dS02-182_WBGene00009620.rds
inst/extdata/rds/relCoord_ampTSS/dS02-182_WBGene00009621.rds
inst/extdata/rds/relCoord_ampTSS/dS02-182_WBGene00009801.rds
inst/extdata/rds/relCoord_ampTSS/dS02-182_WBGene00015947.rds
inst/extdata/rds/relCoord_ampTSS/dS02-182_WBGene00015955.rds
man/SumSqMatrixRows.Rd
man/allClassMeansToGR.Rd
man/canberraDist.Rd
man/classLikelihoodPerRead.Rd
man/classifyAndSortReads.Rd
man/clusterRandomMatrices.Rd
man/combineSilStats.Rd
man/correlationDist.Rd
man/cosineDist.Rd
man/countGenesPerClass.Rd
man/doSingleUMAPplot.Rd
man/em_basic.Rd
man/em_classify.Rd
man/euclideanDist.Rd
man/getAllClassMeansMatrix.Rd
man/getClassMeansMatrix.Rd
man/getClassVote.Rd
man/getDistMatrix.Rd
man/getFullMatrix.Rd
man/getMode.Rd
man/getReadClass.Rd
man/getSilhouetteStats.Rd
man/isMatrixValid.Rd
man/makeDirs.Rd
man/miDist.Rd
man/order_by_prev_cluster.Rd
man/p_converged.Rd
man/p_difference.Rd
man/padEndToRange.Rd
man/padMissingColWithNAs.Rd
man/plotAllClassMeans.Rd
man/plotClassMeans.Rd
man/plotClassMeansWithTracks.Rd
man/plotClassStability.Rd
man/plotClassesSingleMolecule.Rd
man/plotClusteringMetrics.Rd
man/plotEachRepeat.Rd
man/plotFinalClasses.Rd
man/plotGenesPerClass.Rd
man/plotMatPCA.Rd
man/plotMatUMAP.Rd
man/plotPCAofMatrixClasses.Rd
man/plotSmoothedClassMeans.Rd
man/plotUMAPofMatrixClasses.Rd
man/prepareWindows.Rd
man/randomiseMatrixRows.Rd
man/recodeMatrixAsNumeric.Rd
man/reexports.Rd
man/remove0.Rd
man/removeNArows.Rd
man/rescale_0To1.Rd
man/rescale_minus1To1.Rd
man/runClassLikelihoodRpts.Rd
man/runEM.Rd
man/runEMrangeClassNum.Rd
man/runEMrepeats.Rd
man/runEMrepeats_withinSS.Rd
man/selectReadsFromMatrix.Rd
man/silhouettePlot.Rd
man/withinClusterSS.Rd
tests/testthat.R
tests/testthat/test-EMbasic.R
tests/testthat/test-EMmultigene.R
tests/testthat/test-clusterUtils.R
tests/testthat/test-preProcessMethMats.R
tests/testthat/test-utils.R
vignettes/UsingEMclassifieR.R
vignettes/UsingEMclassifieR.Rmd
vignettes/UsingEMclassifieR.html
vignettes/em_demo.Rmd
