TBEST: Tree Branches Evaluated Statistically for Tightness

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Our method introduces mathematically well-defined measures for tightness of branches in a hierarchical tree. Statistical significance of the findings is determined, for all branches of the tree, by performing permutation tests, optionally with generalized Pareto p-value estimation.

Author
Guoli Sun, Alex Krasnitz
Date of publication
2014-12-29 17:56:43
Maintainer
Guoli Sun <guolisun87@gmail.com>
License
GPL-2
Version
5.0

View on CRAN

Man pages

best
An object of class "best"
LeafContent
Find names of leaves belongigng to given branches of a...
leukemia
Leukemia data
partition
An object of class "partition"
PartitionTree
Find the most detailed partition of a tree into tight...
plot.best
Plot a dendrogam of a hierarchical cluster with branches...
SigTree
Perform statistical analysis of tightness for branches of a...
T10
Breast tumor single cells data

Files in this package

TBEST
TBEST/NAMESPACE
TBEST/data
TBEST/data/T10.rda
TBEST/data/leukemia.rda
TBEST/R
TBEST/R/TreeStat.R
TBEST/R/nll.R
TBEST/R/Pgpd.R
TBEST/R/bestmatch.R
TBEST/R/PartitionTree.R
TBEST/R/plot.best.R
TBEST/R/bestmatchl.R
TBEST/R/treetext.R
TBEST/R/Pvalue.R
TBEST/R/RandTail.R
TBEST/R/hc2axes.R
TBEST/R/Ppermest_opt.R
TBEST/R/byfactor.R
TBEST/R/RandTree.R
TBEST/R/SigTree.R
TBEST/R/BootTree.R
TBEST/R/LeafContent.R
TBEST/MD5
TBEST/DESCRIPTION
TBEST/man
TBEST/man/leukemia.Rd
TBEST/man/PartitionTree.Rd
TBEST/man/best.Rd
TBEST/man/T10.Rd
TBEST/man/plot.best.Rd
TBEST/man/LeafContent.Rd
TBEST/man/partition.Rd
TBEST/man/SigTree.Rd