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

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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.

Author
Jan Budczies, Daniel Kosztyla
Date of publication
None
Maintainer
Daniel Kosztyla <danielkossi@hotmail.com>
License
GPL 3
Version
1.18.0

View on Bioconductor

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"

Files in this package

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