RCASPAR: A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
Version 1.22.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorDouaa Mugahid, Lars Kaderali
Bioconductor views GeneExpression Genetics Proteomics Visualization aCGH
Date of publicationNone
MaintainerDouaa Mugahid <douaa.mugahid@gmail.com>, Lars Kaderali <lars.kaderali@uni-greifswald.de>
LicenseGPL (>=3)
Version1.22.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("RCASPAR")

Man pages

Bergamaschi: Gene expression data of 82 patients with 10 genes as...
deriv_weight_estimator_BLH: A function that gives the derivative of the objective...
deriv_weight_estimator_BLH_noprior: A function that gives the derivative of the objective...
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...
weight_estimator_BLH: Returns the value of the objective function used for...
weight_estimator_BLH_noprior: Returns the value of the objective function used for...
weights_BLH: Optimization for the regression coefficients and baseline...
weights_xvBLH: A special version of STpredictor.BLH used within k-xv to...

Functions

kmplt Man page
Bergamaschi Man page
RCASPAR Man page
RCASPAR-package Man page
STpredictor_BLH Man page Source code
STpredictor_xvBLH Man page Source code
deriv_weight_estimator_BLH Man page Source code
deriv_weight_estimator_BLH_noprior Man page Source code
kmplt Source code
kmplt_svrl Man page Source code
logrnk Man page Source code
pltgamma Man page Source code
pltprior Man page Source code
simpson Man page Source code
survData Man page
survivAURC Man page Source code
survivROC Man page Source code
trapezoid Man page Source code
weight_estimator_BLH Man page Source code
weight_estimator_BLH_noprior Man page Source code
weights_BLH Man page Source code
weights_xvBLH Man page Source code

Files

DESCRIPTION
NAMESPACE
R
R/AUC.R
R/STpredictor_BLH.R
R/k-xvBLH.R
R/kmplt.R
R/kmplt_svrl.R
R/logrnk.R
R/pltgamma.R
R/pltprior.R
R/survivAURC.R
R/survivROC.R
R/weightestimator_BLH.R
R/weights_BLH.R
R/weights_xvBLH.R
build
build/vignette.rds
data
data/Bergamaschi.RData
data/survData.RData
inst
inst/doc
inst/doc/RCASPAR.R
inst/doc/RCASPAR.Rnw
inst/doc/RCASPAR.pdf
man
man/Bergamaschi.Rd
man/RCASPAR-package.Rd
man/STpredictor_BLH.Rd
man/STpredictor_xvBLH.Rd
man/deriv_weight_estimator_BLH.rd
man/deriv_weight_estimator_BLH_noprior.rd
man/kmplt.Rd
man/kmplt_svrl.Rd
man/logrnk.Rd
man/pltgamma.Rd
man/pltprior.Rd
man/simpson.Rd
man/survData.Rd
man/survivAURC.Rd
man/survivROC.Rd
man/trapezoid.Rd
man/weight_estimator_BLH.rd
man/weight_estimator_BLH_noprior.rd
man/weights_BLH.rd
man/weights_xvBLH.rd
vignettes
vignettes/RCASPAR.Rnw
vignettes/censor_table.PNG
vignettes/covar_table.PNG
vignettes/functions_fig.PNG
RCASPAR documentation built on May 20, 2017, 9:20 p.m.