Thresher: Threshing and Reaping for Principal Components
Version 0.11.0

The Thresher package defines the classes used to identify outliers (threshing) and compute the number of significant principal components and number of clusters (reaping) in a joint application of PCA and hierarchical clustering.

Browse man pages Browse package API and functions Browse package files

AuthorKevin R. Coombes
Bioconductor views Clustering
Date of publication2017-04-26 13:06:46
MaintainerKevin R. Coombes <krc@silicovore.com>
LicenseApache License (== 2.0)
Version0.11.0
URL http://oompa.r-forge.r-project.org/
Package repositoryView on R-Forge
InstallationInstall the latest version of this package by entering the following in R:
install.packages("Thresher", repos="http://R-Forge.R-project.org")

Man pages

fit-or-miss-class: Class '"fit or miss"'
getColors-methods: ~~ Methods for Function 'getColors' ~~
getSplit-methods: ~~ Methods for Function 'getSplit' ~~
heat-methods: ~~ Methods for Function 'heat' ~~
image-methods: ~~ Methods for Function 'image' ~~
makeFigures-methods: ~~ Methods for Function 'makeFigures' ~~
matchLabels: Match Arbitrary Class Assignments Across Methods
movMF-class: Class '"movMF"'
number-or-miss-class: Class '"number or miss"'
palettes: Color Palettes Used By Thresher Classes
plot-methods: ~~ Methods for Function 'plot' ~~
Reaper: Reaper
Reaper-class: Class '"Reaper"'
scatter-methods: ~~ Methods for Function 'scatter' ~~
screeplot-methods: ~~ Methods for Function 'screeplot' ~~
SignalSet-class: Class '"SignalSet"'
SimThresher: simt
SimThresher-class: Class '"SimThresher"'
summary-methods: ~~ Methods for Function 'summary' ~~
Thresher: Thresher
Thresher-class: Class '"Thresher"'
Thresher-package: What the package does (short line) Threshing and Reaping for...
unitize: Convert a Vector to Unit Length

Functions

Reaper Man page Source code
Reaper-class Man page
SignalSet-class Man page
SimThresher Man page Source code
SimThresher-class Man page
Thresher Man page Man page Source code
Thresher-class Man page
Thresher-package Man page
bestMetric Man page Source code
countAgreement Man page Source code
findSignals Source code
fit or miss-class Man page
fitModels Source code
getColors,Reaper-method Man page Man page
getColors,Thresher-method Man page Man page
getColors-methods Man page
getSplit,Reaper-method Man page Man page
getSplit,Thresher-method Man page Man page
getSplit-methods Man page
heat,Thresher-method Man page Man page
heat-methods Man page
image,SimThresher-method Man page Man page
image-methods Man page
labelAccuracy Man page Source code
labelMatcher Man page Source code
makeColorScheme Source code
makeFigures,Reaper-method Man page Man page
makeFigures,SimThresher-method Man page Man page
makeFigures,Thresher-method Man page Man page
makeFigures-methods Man page
matchLabels Man page Source code
movMF-class Man page
number or miss-class Man page
plot,AuerGervini,missing-method Man page
plot,Thresher,missing-method Man page Man page
plot-methods Man page
samplePalette Man page
scatter,Thresher-method Man page Man page
scatter-methods Man page
screeplot,Thresher-method Man page Man page
screeplot-methods Man page
spand Source code
summary,AuerGervini-method Man page
summary-methods Man page
thresherPalette Man page
unitize Man page Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/01-labelMatcher.R
R/02-thresher.R
R/03-SimThesher.R
R/04-reaper.R
TODO
data
data/savedSims.rda
man
man/Reaper-class.Rd
man/Reaper.Rd
man/SignalSet-class.Rd
man/SimThresher-class.Rd
man/SimThresher.Rd
man/Thresher-class.Rd
man/Thresher-package.Rd
man/Thresher.Rd
man/fit-or-miss-class.Rd
man/getColors-methods.Rd
man/getSplit-methods.Rd
man/heat-methods.Rd
man/image-methods.Rd
man/makeFigures-methods.Rd
man/matchLabels.Rd
man/movMF-class.Rd
man/number-or-miss-class.Rd
man/palettes.Rd
man/plot-methods.Rd
man/scatter-methods.Rd
man/screeplot-methods.Rd
man/summary-methods.Rd
man/unitize.Rd
tests
tests/00-Auer-Gervini_final.txt
tests/01-label.R
tests/01-label.Rout.save
tests/02-thresh.R
tests/02-thresh.Rout.save
tests/02-thresher_final.txt
tests/04-reap.R
tests/04-reap.Rout.save
Thresher documentation built on May 21, 2017, 12:33 a.m.