Man pages for hdng/clonevol
Clonal ordering and visualization

adjust.clone.vafAdjust clone VAF according to significant different test...
assign.events.to.clonesWrapper to assign events to clones in all merged trees This...
assign.events.to.clones.of.a.treeAssign events to clones based on presence/absence of them...
boot.vaf.ciCalculate CI for a cluster in a sample
clone.vaf.diffTest if two clones have different VAFs Deprecated!
compare.clone.treesCompare two clonal evolution trees
compare.clone.trees.removing.leavesCompare two merged clonal evolution trees
convert.clone.to.branchCreate a tree from the merged.tree data.frame in clonevol...
convert.consensus.tree.clone.to.branchCreate trees for all merged.trees in clonevol output
createFishPlotObjectsCreate a list of fishplot objects that can then be called
cross.rule.scoreApply cross rule to all clones in all matched models using...
cutBigValueReplace values bigger than a cutoff by a value
determine.subcloneDetermine which clones are subclone in a single sample, also...
draw.branchDraw tree branch using polygon that allows for choosing...
draw.cloneDraw a bell/polygon representing a clone evolution, annotated...
draw.sample.clonesDraw clonal structures/evolution of a single sample
draw.sample.clones.allDraw all enumerated clonal models for a single sample
enumerate.clonesEnumerate all possible clonal structures for a single sample,...
estimate.ccfCalculate CI of CCF, pvals, etc.
estimate.clone.vafEstimate VAFs of clones/clusters from clonality analysis...
extract.mapped.eventsProduce a data frame of events mapped to clone and associated...
find.matched.modelsFind matched models between samples infer clonal evolution...
generate.bootGenerate and calculate bootstrap means for all clusters
generate.boot.nonparametricGenerate and calculate bootstrap means for all clusters...
generate.cloud.of.cellsGenerate a cloud of circles to represent cell population
generate.fill.pointsGenerate fill points for bell/polygon plots
generateFishplotInputsGenerate fishplot ready data from clonevol clonal evolution...
germinateGerminate a seed.
get.cell.frac.ciGet cellular fraction confidence interval
get.clonevol.colorsGet the hex string of the preset colors optimized for...
get.model.max.p.valueGet the highest p.value of the test of Ho:ccf<0 This is the...
get.model.non.negative.ccf.probGet probability of a model for a sample as the product of...
get.subclones.across.samplesGet all set of subclones for all clone across samples...
import.treeImport trees to clonevol
infer.clonal.modelsInfer clonal structures and evolution models for multiple...
insert.lfInsert line feed
is.ancestorCheck if clone a is ancestor of clone b in the clonal...
make.clonal.data.frameCreate a data frame to hold clonal structure of a single...
make.graphConstruct igraph object from clonal structures of a sample
match.sample.clonesCheck if two clonal structures are compatible (one evolves to...
merge.all.matched.clone.treesRecreate merged trees for matched models, given output of...
merge.clone.treesMerge clonnal evolution trees from multiple samples into a...
merge.samplesMerge multi region samples into a meta sample
merge.variants.and.eventsMerge variants and mapped events onto the same data frame...
plot.all.trees.clone.as.branchPlot all branch-based consensus clonal evolution trees
plot.cell.populationPlot a tumor as a cloud of cells reflecting the cellular...
plot.clonal.modelsVisualize clonal evolution models using various plots.
plot.clonevol.colorsPlot ClonEvol colors
plot.cloud.of.cellsPlot a cloud of cells
plot.cluster.flowPlot the mean/median of the clusters of variants across...
plot.pairwisePlot values of columns pairwise
plot.plantPlot method for plant objects.
plot.treePlot clonal evolution tree
plot.tree.clone.as.branchPlot a consensus tree using branch-based visualization
plot.variant.clustersPlot variant clustering using combination of box, violin, and...
replaceNAReplace NA with some value
rescale.vafRescale VAF of subclones for visualzation purpose
save.clonevol.resultsSave clonevol output to file
scale.cell.fracScale cellular fraction in a clonal architecture model
scale.sample.positionPrepare x positions to layout samples in bell plots
set.positionSet vertical position of clones within a sample clonal...
subclonal.testSubclonal test of H0:
transfer.events.to.consensus.treesTransfer driver variants/events from the cluster onto the...
trim.clone.treesReduce clone trees to core trees after excluding clones that...
write.treeWrite clonal evolution tree to file TODO: do!
hdng/clonevol documentation built on Sept. 14, 2017, 5:46 a.m.