HCsnip: Semi-supervised adaptive-height snipping of the Hierarchical Clustering tree

Decompose given hierarchical clustering tree into non-overlapping clusters in a semi-supervised way by using available patients follow-up information as guidance. Contains functions for snipping HC tree, various cluster quality evaluation criteria, assigning new patients to one of the two given HC trees, testing the significance of clusters with permutation argument and clusters visualization using sample's molecular entropy.

Author
Askar Obulkasim
Date of publication
None
Maintainer
Askar Obulkasim <askar703@gmail.com>
License
GPL (>= 2)
Version
1.14.0

View on Bioconductor

Man pages

BullingerLeukemia
Leukemia data
cluster_pred
Semi-supervised clustering
EnvioPlot
Visualize cluster's molecular entropy by violin plot
HCsnip-package
Semi-supervised adaptive-height snipping of the Hierarchical...
HCsnipper
HC tree snipper
measure
Evaluate cluster quality
perm_test
A function to select an optimal partition (clustering) from...
RSF_eval
Function to calculate error rate using the Random Survival...
surv_measure
Cluster quality evaluation using follow-up data
TcgaGBM
Glioblastoma multiforme gene expression data
TwoHC_assign
Function to assign new samples to one of the two given...
TwoHC_perm
Function to assess the significance of group assignmetn from...

Files in this package

HCsnip/DESCRIPTION
HCsnip/NAMESPACE
HCsnip/R
HCsnip/R/EnvioPlot.R
HCsnip/R/HCsnipper.R
HCsnip/R/RSF_eval.R
HCsnip/R/TwoHC_assign.R
HCsnip/R/TwoHC_perm.R
HCsnip/R/cluster_pred.R
HCsnip/R/measure.R
HCsnip/R/perm_test.R
HCsnip/R/private.R
HCsnip/R/surv_measure.R
HCsnip/build
HCsnip/build/vignette.rds
HCsnip/data
HCsnip/data/BullingerLeukemia.rda
HCsnip/data/TcgaGBM.rda
HCsnip/data/datalist
HCsnip/inst
HCsnip/inst/doc
HCsnip/inst/doc/HCsnip.R
HCsnip/inst/doc/HCsnip.Rnw
HCsnip/inst/doc/HCsnip.pdf
HCsnip/man
HCsnip/man/BullingerLeukemia.Rd
HCsnip/man/EnvioPlot.Rd
HCsnip/man/HCsnip-package.Rd
HCsnip/man/HCsnipper.Rd
HCsnip/man/RSF_eval.Rd
HCsnip/man/TcgaGBM.Rd
HCsnip/man/TwoHC_assign.Rd
HCsnip/man/TwoHC_perm.Rd
HCsnip/man/cluster_pred.Rd
HCsnip/man/measure.Rd
HCsnip/man/perm_test.Rd
HCsnip/man/surv_measure.Rd
HCsnip/vignettes
HCsnip/vignettes/HCsnip.Rnw
HCsnip/vignettes/Rank.pdf
HCsnip/vignettes/densityR.pdf
HCsnip/vignettes/entropy.pdf