cancerclass: Development and validation of diagnostic tests from high-dimensional molecular data
Version 1.20.0

The classification protocol starts with a feature selection step and continues with nearest-centroid classification. The accurarcy of the predictor can be evaluated using training and test set validation, leave-one-out cross-validation or in a multiple random validation protocol. Methods for calculation and visualization of continuous prediction scores allow to balance sensitivity and specificity and define a cutoff value according to clinical requirements.

Browse man pages Browse package API and functions Browse package files

AuthorJan Budczies, Daniel Kosztyla
Bioconductor views Cancer Classification Microarray Visualization
Date of publicationNone
MaintainerDaniel Kosztyla <danielkossi@hotmail.com>
LicenseGPL 3
Version1.20.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("cancerclass")

Man pages

cancerclass-internal: Internal Functions in the cancerclass Package
cancerclass-package: Development and validation of diagnostic tests from...
fit: Fitting of a predictor
GOLUB: GOLUB DATA
loo: Leave-one-out cross-validation
nvalidate: Classification in a multiple random validation protocol in...
nvalidation-class: Class "nvalidation"
plot: Plot Method for 'validation, nvalidation, prediction,...
plot3d: Plot3d method for 'validtion and 'nvalidation' classes
prediction-class: Class "prediction"
predictor-class: Class "predictor"
predict,predictor-method: Predict Method for 'predictor' Class
summary,prediction-method: Summary Method for 'prediction' Class
validate: Classification in a Multiple Random Validation Protocol in...
validation-class: Class "validation"

Functions

GOLUB Man page
GOLUB1 Man page
calc.auc Man page Source code
calc.roc Man page Source code
cancerclass Man page
cancerclass-internal Man page
filter Man page Source code
fit Man page Source code
get.d Man page Source code
get.d2 Man page Source code
get.lm Man page Source code
get.ntrain Man page Source code
get.prop Man page Source code
ilogit Man page Source code
loo Man page Source code
nitFoo Source code
nvalidate Man page Source code
nvalidation-class Man page
onLoad Source code
plot Man page
plot,nvalidation-method Man page
plot,prediction-method Man page
plot,predictor-method Man page
plot,validation-method Man page
plot3d Man page
plot3d,nvalidation-method Man page
plot3d,validation-method Man page
predict Man page
predict,predictor-method Man page
predict-methods Man page
prediction-class Man page
predictor-class Man page
prepare Man page Source code
summary Man page
summary,ANY-method Man page
summary,prediction-method Man page
summary-methods Man page
validate Man page Source code
validation-class Man page

Files

DESCRIPTION
NAMESPACE
R
R/cancerclass-internal.R
R/fit.R
R/loo.R
R/nvalidate.R
R/nvalidation-class.R
R/plot3d_nvalidation.R
R/plot3d_validation.R
R/plot_nvalidation.R
R/plot_prediction.R
R/plot_predictor.R
R/plot_validation.R
R/predict_predictor.R
R/prediction-class.R
R/predictor-class.R
R/summary_prediction.R
R/validate.R
R/validation-class.R
build
build/vignette.rds
data
data/GOLUB.RData
data/GOLUB1.RData
data/datalist
inst
inst/doc
inst/doc/vignette_cancerclass.R
inst/doc/vignette_cancerclass.Rnw
inst/doc/vignette_cancerclass.pdf
man
man/GOLUB.Rd
man/cancerclass-internal.Rd
man/cancerclass-package.Rd
man/fit.Rd
man/loo.Rd
man/nvalidate.Rd
man/nvalidation-class.Rd
man/plot.Rd
man/plot3d.Rd
man/predict,predictor-method.Rd
man/prediction-class.Rd
man/predictor-class.Rd
man/summary,prediction-method.Rd
man/validate.Rd
man/validation-class.Rd
src
src/copa.c
src/copa.h
src/cor.c
src/cor.h
src/fc.c
src/fc.h
src/help.c
src/help.h
src/ort.c
src/ort.h
src/os.c
src/os.h
src/shift.c
src/shift.h
src/statistics.c
src/student.c
src/student.h
src/throw.c
src/throw.h
src/welch.c
src/welch.h
src/wilcox.c
src/wilcox.h
vignettes
vignettes/vignette_cancerclass.Rnw
cancerclass documentation built on May 20, 2017, 10:29 p.m.