RCASPAR: A package for survival time prediction based on a piecewise baseline hazard Cox regression model.

The package is the R-version of the C-based software \bold{CASPAR} (Kaderali,2006: \url{http://bioinformatics.oxfordjournals.org/content/22/12/1495}). It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. The model is a piecewise baseline hazard Cox regression model with an Lq-norm based prior that selects for the most important regression coefficients, and in turn the most relevant covariates for survival analysis. It was primarily tried on gene expression and aCGH data, but can be used on any other type of high-dimensional data and in disciplines other than biology and medicine.

Author
Douaa Mugahid, Lars Kaderali
Date of publication
None
Maintainer
Douaa Mugahid <douaa.mugahid@gmail.com>, Lars Kaderali <lars.kaderali@uni-greifswald.de>
License
GPL (>=3)
Version
1.20.0

View on Bioconductor

Man pages

Bergamaschi
Gene expression data of 82 patients with 10 genes as...
kmplt
Plot Kaplan Meier curve
kmplt_svrl
A function that plots the KM curves of $2-3$ patient sets in...
logrnk
Performs Log Rank test on the long and short patient sets
pltgamma
Plotting the gamma distribution of shape parameter
pltprior
A function to visualize the shape of the prior on the weights...
RCASPAR-package
A package for survival time prediction based on a piecewise...
simpson
A function that calculates the area under a curve based on...
STpredictor_BLH
Predicts the survival times of the validation set based on...
STpredictor_xvBLH
This function performs a cross validation on the full data...
survData
Survial data of 82 patients
survivAURC
A function that calculates the area under a curve constructed...
survivROC
Generates the ROC curve at a given time point given the...
trapezoid
A function that calculates the area under a curve based on...

Files in this package

RCASPAR/DESCRIPTION
RCASPAR/NAMESPACE
RCASPAR/R
RCASPAR/R/AUC.R
RCASPAR/R/STpredictor_BLH.R
RCASPAR/R/k-xvBLH.R
RCASPAR/R/kmplt.R
RCASPAR/R/kmplt_svrl.R
RCASPAR/R/logrnk.R
RCASPAR/R/pltgamma.R
RCASPAR/R/pltprior.R
RCASPAR/R/survivAURC.R
RCASPAR/R/survivROC.R
RCASPAR/R/weightestimator_BLH.R
RCASPAR/R/weights_BLH.R
RCASPAR/R/weights_xvBLH.R
RCASPAR/build
RCASPAR/build/vignette.rds
RCASPAR/data
RCASPAR/data/Bergamaschi.RData
RCASPAR/data/survData.RData
RCASPAR/inst
RCASPAR/inst/doc
RCASPAR/inst/doc/RCASPAR.R
RCASPAR/inst/doc/RCASPAR.Rnw
RCASPAR/inst/doc/RCASPAR.pdf
RCASPAR/man
RCASPAR/man/Bergamaschi.Rd
RCASPAR/man/RCASPAR-package.Rd
RCASPAR/man/STpredictor_BLH.Rd
RCASPAR/man/STpredictor_xvBLH.Rd
RCASPAR/man/deriv_weight_estimator_BLH.rd
RCASPAR/man/deriv_weight_estimator_BLH_noprior.rd
RCASPAR/man/kmplt.Rd
RCASPAR/man/kmplt_svrl.Rd
RCASPAR/man/logrnk.Rd
RCASPAR/man/pltgamma.Rd
RCASPAR/man/pltprior.Rd
RCASPAR/man/simpson.Rd
RCASPAR/man/survData.Rd
RCASPAR/man/survivAURC.Rd
RCASPAR/man/survivROC.Rd
RCASPAR/man/trapezoid.Rd
RCASPAR/man/weight_estimator_BLH.rd
RCASPAR/man/weight_estimator_BLH_noprior.rd
RCASPAR/man/weights_BLH.rd
RCASPAR/man/weights_xvBLH.rd
RCASPAR/vignettes
RCASPAR/vignettes/RCASPAR.Rnw
RCASPAR/vignettes/censor_table.PNG
RCASPAR/vignettes/covar_table.PNG
RCASPAR/vignettes/functions_fig.PNG