API for hdng/clonevol
Clonal ordering and visualization

Global functions
adjust.clone.vaf Man page Source code
assign.events.to.clones Man page Source code
assign.events.to.clones.of.a.tree Man page Source code
boot.vaf.ci Man page Source code
clone.vaf.diff Man page Source code
combine.p Source code
compare.clone.trees Man page Source code
compare.clone.trees.removing.leaves Man page Source code
convert.clone.to.branch Man page Source code
convert.consensus.tree.clone.to.branch Man page Source code
convert.merged.tree.clone.to.branch Source code
createFishPlotObjects Man page Source code
cross.rule.score Man page Source code
cutBigValue Man page Source code
determine.subclone Man page Source code
draw.branch Man page Source code
draw.clone Man page Source code
draw.sample.clones Man page Source code
draw.sample.clones.all Man page Source code
enumerate.clones Man page Source code
estimate.ccf Man page Source code
estimate.clone.vaf Man page Source code
extract.mapped.events Man page Source code
fertilise Source code
find.matched.models Man page Source code
fisher.p Source code
generate.boot Man page Source code
generate.boot.nonparametric Man page Source code
generate.cloud.of.cells Man page Source code
generate.fill.points Man page Source code
generateFishplotInputs Man page Source code
germinate Man page Source code
get.cell.frac.ci Man page Source code
get.clonevol.colors Man page Source code
get.ggplot2.colors Source code
get.mean Source code
get.median Source code
get.model.max.p.value Man page Source code
get.model.non.negative.ccf.prob Man page Source code
get.model.score Source code
get.n Source code
get.subclones.across.samples Man page Source code
get.xy Source code
import.tree Man page Source code
infer.clonal.models Man page Source code
insert.lf Man page Source code
is.ancestor Man page Source code
is.poly Source code
make.clonal.data.frame Man page Source code
make.graph Man page Source code
match.sample.clones Man page Source code
merge.all.matched.clone.trees Man page Source code
merge.clone.trees Man page Source code
merge.samples Man page Source code
merge.variants.and.events Man page Source code
multiplot Source code
plot.all.trees.clone.as.branch Man page Source code
plot.cell.population Man page Source code
plot.clonal.models Man page Source code
plot.clonevol.colors Man page Source code
plot.cloud.of.cells Man page Source code
plot.cluster.flow Man page Source code
plot.pairwise Man page Source code
plot.plant Man page Source code
plot.tree Man page Source code
plot.tree.clone.as.branch Man page Source code
plot.variant.clusters Man page Source code
randomizeHjust Source code
replaceNA Man page Source code
resample.test.greater Source code
resample.test.pooled Source code
rescale.vaf Man page Source code
run.1sample.example Source code
run.3samples.example Source code
run.AML31 Source code
run.AML31.bootstrap Source code
save.clonevol.results Man page Source code
scale.cell.frac Man page Source code
scale.sample.position Man page Source code
set.position Man page Source code
subclonal.test Man page Source code
sum.polyclonal Source code
transfer.events.to.consensus.trees Man page Source code
trim.clone.trees Man page Source code
vaf2ccf Source code
variant.box.plot Source code
write.tree Man page Source code
hdng/clonevol documentation built on Sept. 14, 2017, 5:46 a.m.