ClusterSignificance: The ClusterSignificance package provides tools to assess if clusters have a separation different from random or permuted data

The ClusterSignificance package provides tools to assess if clusters have a separation different from random or permuted data. ClusterSignificance investigates clusters of two or more groups by first, projecting all points onto a one dimensional line. Cluster separations are then scored and the probability of the seen separation being due to chance is evaluated using a permutation method.

AuthorJason T. Serviss and Jesper R. Gadin
Date of publicationNone
MaintainerJason T Serviss <jason.serviss@ki.se>
LicenseGPL-3
Version1.2.3

View on Bioconductor

Functions

ClassifiedPoints Man page
.ClassifiedPoints Man page
ClassifiedPoints-class Man page
classify Man page
classify Man page
classify,Mlp-method Man page
classify,Mlp-method Man page
classify,Pcp-method Man page
classify,Pcp-method Man page
ClusterSignificance Man page
ClusterSignificance-package Man page
c,PermutationResults-method Man page
getData Man page
getData,ClassifiedPoints-method Man page
getData,Mlp-method Man page
getData,Pcp-method Man page
getData,PermutationResults-method Man page
initialize,ClassifiedPoints-method Man page
initialize,Mlp-method Man page
initialize,Pcp-method Man page
initialize,PermutationResults-method Man page
mlp Man page
mlp Man page
Mlp Man page
.Mlp Man page
Mlp-class Man page
mlpMatrix Man page
mlp,matrix-method Man page
mlp,matrix-method Man page
pcp Man page
pcp Man page
Pcp Man page
.Pcp Man page
Pcp-class Man page
pcpMatrix Man page
pcp,matrix-method Man page
pcp,matrix-method Man page
.PermutationResults Man page
PermutationResults-class Man page
permute Man page
permute Man page
permute,matrix-method Man page
permute,matrix-method Man page
plot,ClassifiedPoints,missing-method Man page
plot,Mlp,missing-method Man page
plot,Pcp,missing-method Man page
plot,PermutationResults,missing-method Man page
pvalue Man page
pvalue,PermutationResults-method Man page
show,ClassifiedPoints-method Man page
show,Mlp-method Man page
show,Pcp-method Man page
show,PermutationResults-method Man page

Files

ClusterSignificance/.travis.yml
ClusterSignificance/DESCRIPTION
ClusterSignificance/NAMESPACE
ClusterSignificance/NEWS
ClusterSignificance/R
ClusterSignificance/R/All-classes.R ClusterSignificance/R/ClusterSignificance-package.R ClusterSignificance/R/classifier-methods.R ClusterSignificance/R/initialize-methods.R ClusterSignificance/R/mlpMatrix.R ClusterSignificance/R/pcpMatrix.R ClusterSignificance/R/permutation-methods.R ClusterSignificance/R/plot-methods.R ClusterSignificance/R/projection-methods.R ClusterSignificance/R/show-methods.R
ClusterSignificance/README.md
ClusterSignificance/build
ClusterSignificance/build/vignette.rds
ClusterSignificance/data
ClusterSignificance/data/mlpMatrix.rda
ClusterSignificance/data/pcpMatrix.rda
ClusterSignificance/inst
ClusterSignificance/inst/data-raw
ClusterSignificance/inst/data-raw/demoData.R
ClusterSignificance/inst/doc
ClusterSignificance/inst/doc/ClusterSignificance-vignette.R
ClusterSignificance/inst/doc/ClusterSignificance-vignette.Rmd
ClusterSignificance/inst/doc/ClusterSignificance-vignette.html
ClusterSignificance/man
ClusterSignificance/man/ClusterSignificance-package.Rd ClusterSignificance/man/classify.Rd ClusterSignificance/man/mlp.Rd ClusterSignificance/man/mlpMatrix.Rd ClusterSignificance/man/pcp.Rd ClusterSignificance/man/pcpMatrix.Rd ClusterSignificance/man/permute.Rd
ClusterSignificance/tests
ClusterSignificance/tests/testthat
ClusterSignificance/tests/testthat.R
ClusterSignificance/tests/testthat/test_classifier-methods.R
ClusterSignificance/tests/testthat/test_permutation-methods.R
ClusterSignificance/tests/testthat/test_plot-methods.R
ClusterSignificance/tests/testthat/test_projection-methods.R
ClusterSignificance/vignettes
ClusterSignificance/vignettes/ClusterSignificance-vignette.Rmd

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.