Files in TRONCO

TRONCO, an R package for TRanslational ONCOlogy

R/edmonds.algorithm.R R/editing.functions.R R/statistics.R R/external.R R/chow.liu.algorithm.R R/which.functions.R R/bootstrap.R R/capri.algorithm.R R/loading.R R/gabow.algorithm.R R/capri.hypotheses.R R/prim.algorithm.R R/visualization.R R/zzz.R R/caprese.algorithm.R R/selection.R R/tronco.R R/data.R R/lregfit.R R/create.model.R R/as.functions.R R/correctness.R vignettes/4_data_manipulation.Rmd vignettes/6_post_reconstruction.Rmd vignettes/1_introduction.Rmd vignettes/5_model_inference.Rmd vignettes/7_import_export.Rmd vignettes/3_data_visualization.Rmd vignettes/2_loading_data.Rmd man/oncoprint.Rd man/import.model.Rd man/hypothesis.add.homologous.Rd man/enforce.string.Rd man/as.kfold.eloss.Rd man/cbio.query.Rd man/delete.samples.Rd man/hypothesis.add.group.Rd man/samples.selection.Rd man/as.colors.Rd man/delete.model.Rd man/export.graphml.Rd man/as.genes.Rd man/tronco.pattern.plot.Rd man/TCGA.remove.multiple.samples.Rd man/pheatmap.Rd man/as.gene.Rd man/trim.Rd man/npatterns.Rd man/tronco.capri.Rd man/as.genes.in.patterns.Rd man/tronco.plot.Rd man/pathway.visualization.Rd man/tronco.kfold.posterr.Rd man/crc_plain.Rd man/export.mutex.Rd man/as.types.Rd man/test_model.Rd man/as.parameters.Rd man/extract.MAF.HuGO.Entrez.map.Rd man/as.confidence.Rd man/tronco.caprese.Rd man/ngenes.Rd man/rename.gene.Rd man/nameToKey.Rd man/muts.Rd man/annotate.description.Rd man/has.model.Rd man/AND.Rd man/events.selection.Rd man/tronco.chowliu.Rd man/tronco.gabow.Rd man/test_model_kfold.Rd man/delete.pattern.Rd man/tronco.bootstrap.Rd man/as.genotypes.Rd man/duplicates.Rd man/maf.Rd man/test_dataset_no_hypos.Rd man/change.color.Rd man/import.mutex.groups.Rd man/hypothesis.add.Rd man/as.kfold.posterr.Rd man/as.hypotheses.Rd man/as.models.Rd man/consolidate.data.Rd man/stage.Rd man/view.Rd man/genes.table.report.Rd man/keysToNames.Rd man/join.types.Rd man/intersect.datasets.Rd man/annotate.stages.Rd man/as.conditional.probs.Rd man/test_dataset.Rd man/export.nbs.input.Rd man/as.samples.Rd man/ebind.Rd man/crc_maf.Rd man/delete.event.Rd man/order.frequency.Rd man/tronco.kfold.prederr.Rd man/ssplit.Rd man/import.GISTIC.Rd man/as.types.in.patterns.Rd man/tronco.edmonds.Rd man/as.bootstrap.scores.Rd man/delete.type.Rd man/which.samples.Rd man/as.events.in.sample.Rd man/sbind.Rd man/enforce.numeric.Rd man/crc_gistic.Rd man/XOR.Rd man/as.kfold.prederr.Rd man/as.events.in.patterns.Rd man/as.adj.matrix.Rd man/OR.Rd man/as.events.Rd man/has.stages.Rd man/as.selective.advantage.relations.Rd man/import.genotypes.Rd man/as.joint.probs.Rd man/ntypes.Rd man/as.marginal.probs.Rd man/nsamples.Rd man/aCML.Rd man/rank.recurrents.Rd man/rename.type.Rd man/has.duplicates.Rd man/as.description.Rd man/is.compliant.Rd man/nhypotheses.Rd man/nevents.Rd man/import.MAF.Rd man/oncoprint.cbio.Rd man/as.alterations.Rd man/as.patterns.Rd man/as.pathway.Rd man/tronco.kfold.eloss.Rd man/join.events.Rd man/delete.gene.Rd man/tronco.prim.Rd man/TCGA.map.clinical.data.Rd man/as.stages.Rd man/delete.hypothesis.Rd man/TCGA.multiple.samples.Rd man/TCGA.shorten.barcodes.Rd tests/testthat.R tests/testthat/test_as_function.R tests/testthat/test_statistics.R tests/testthat/test_editing.R tests/testthat/test_tronco.R tests/testthat/test_hypotheses.R tests/testthat/test_visualization.R inst/doc/vignette.R inst/doc/vignette.pdf