SPreFuGED: Selecting a Predictive Function for a Given Gene Expression Data

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The recent advancement of high-throughput technologies has led to frequent utilization of gene expression and other "omics" data for toxicological, diagnostic or prognostic studies in and clinical applications. Unlike in classical predictions where the number of samples is greater than the number of variables (n>p), the challenge faced with prediction using "omics" data is that the number of parameters greatly exceeds the number of samples (p>>n). To solve this curse of dimensionality problem, several predictive functions have been proposed for direct and probabilistic classification and survival predictions. Nevertheless, these predictive functions have been shown to perform differently across datasets. Comparing predictive functions and choosing the best is computationally intensive and leads to selection bias. Thus, the question which function should one choose for a given dataset is to be ascertained. This package implements the approach proposed by Jong et al., (2016) to address this question.

Author
Victor L Jong, Kit CB Roes & Marinus JC Eijkemans
Date of publication
2016-07-29 12:35:58
Maintainer
Victor L Jong <v.l.jong@umcutrecht.nl>
License
GPL (>= 2)
Version
1.0

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Man pages

avAcc
Average accuracy data
covMat
A covariance matrix generating function.
directClass
A function to build and evaluate 10 different classification...
estimateDataCha
A function to estimate data characteristics
fitLMEModel
A function to fit a linear mixed effects (LME) model of...
generateGED
A function to simulate two groups gene expression data (GED)
plotDirectClass
A plotting function for the performance (Accuracy) of direct...
plotSPreFu
A plotting function of the predicted performance of...
SPreFu
A function for selecting an optimal predictive function for a...
SPreFuGED-package
\Sexpr[results=rd,stage=build]{tools:::Rd_package_title("SPreFuGED")}

Files in this package

SPreFuGED
SPreFuGED/NAMESPACE
SPreFuGED/data
SPreFuGED/data/avAcc.RData
SPreFuGED/R
SPreFuGED/R/plotDirectClass.R
SPreFuGED/R/covMat.R
SPreFuGED/R/fitLMEModel.R
SPreFuGED/R/SPreFu.R
SPreFuGED/R/directClass.R
SPreFuGED/R/estimateDataCha.R
SPreFuGED/R/plotSPreFu.R
SPreFuGED/R/generateGED.R
SPreFuGED/MD5
SPreFuGED/build
SPreFuGED/build/partial.rdb
SPreFuGED/DESCRIPTION
SPreFuGED/man
SPreFuGED/man/plotSPreFu.Rd
SPreFuGED/man/directClass.Rd
SPreFuGED/man/SPreFu.Rd
SPreFuGED/man/estimateDataCha.Rd
SPreFuGED/man/plotDirectClass.Rd
SPreFuGED/man/avAcc.Rd
SPreFuGED/man/generateGED.Rd
SPreFuGED/man/SPreFuGED-package.Rd
SPreFuGED/man/covMat.Rd
SPreFuGED/man/fitLMEModel.Rd