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

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.

AuthorJan Budczies, Daniel Kosztyla
Date of publicationNone
MaintainerDaniel Kosztyla <danielkossi@hotmail.com>
LicenseGPL 3
Version1.18.0

View on Bioconductor

Functions

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

Files

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

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

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