Files in hdng/clonevol

Clonal ordering and visualization

R/boxplot.r R/clonevol.r R/clonevol2fishplot.r R/examples.r R/generate.boot.r R/io.r R/stat.r R/trees.package.r R/trees.r R/utils.r R/wrappers.r README.md examples/aml1.r man/adjust.clone.vaf.Rd man/assign.events.to.clones.Rd man/assign.events.to.clones.of.a.tree.Rd man/boot.vaf.ci.Rd man/clone.vaf.diff.Rd man/compare.clone.trees.Rd man/compare.clone.trees.removing.leaves.Rd man/convert.clone.to.branch.Rd man/convert.consensus.tree.clone.to.branch.Rd man/createFishPlotObjects.Rd man/cross.rule.score.Rd man/cutBigValue.Rd man/determine.subclone.Rd man/draw.branch.Rd man/draw.clone.Rd man/draw.sample.clones.Rd man/draw.sample.clones.all.Rd man/enumerate.clones.Rd man/estimate.ccf.Rd man/estimate.clone.vaf.Rd man/extract.mapped.events.Rd man/find.matched.models.Rd man/generate.boot.Rd man/generate.boot.nonparametric.Rd man/generate.cloud.of.cells.Rd man/generate.fill.points.Rd man/generateFishplotInputs.Rd man/germinate.Rd man/get.cell.frac.ci.Rd man/get.clonevol.colors.Rd man/get.model.max.p.value.Rd man/get.model.non.negative.ccf.prob.Rd man/get.subclones.across.samples.Rd man/import.tree.Rd man/infer.clonal.models.Rd man/insert.lf.Rd man/is.ancestor.Rd man/make.clonal.data.frame.Rd man/make.graph.Rd man/match.sample.clones.Rd man/merge.all.matched.clone.trees.Rd man/merge.clone.trees.Rd man/merge.samples.Rd man/merge.variants.and.events.Rd man/plot.all.trees.clone.as.branch.Rd man/plot.cell.population.Rd man/plot.clonal.models.Rd man/plot.clonevol.colors.Rd man/plot.cloud.of.cells.Rd man/plot.cluster.flow.Rd man/plot.pairwise.Rd man/plot.plant.Rd man/plot.tree.Rd man/plot.tree.clone.as.branch.Rd man/plot.variant.clusters.Rd man/replaceNA.Rd man/rescale.vaf.Rd man/save.clonevol.results.Rd man/scale.cell.frac.Rd man/scale.sample.position.Rd man/set.position.Rd man/subclonal.test.Rd man/transfer.events.to.consensus.trees.Rd man/trim.clone.trees.Rd man/write.tree.Rd simulations/sim.r vignettes/clonevol.Rmd vignettes/clonevol.pdf