HybridMTest: Hybrid Multiple Testing
Version 1.20.0

Performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using empirical Bayes probability (EBP) estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weigth. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs.

AuthorStan Pounds <stanley.pounds@stjude.org>, Demba Fofana <demba.fofana@stjude.org>
Bioconductor views GeneExpression Genetics Microarray
Date of publicationNone
MaintainerDemba Fofana <demba.fofana@stjude.org>
LicenseGPL Version 2 or later
Version1.20.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("HybridMTest")

Getting started

Package overview

Popular man pages

correlation.data: Sample ExpressionSet object of correlation.data
grenander.ebp: Grenander EBP.
hybrid.test: Hybrid Multiple Testing of Gene Expression Data
row.kgrp.shapiro: Shapiro Wilk test of normality.
row.kruskal.wallis: Apply the Kruskal-Wallis test many times
row.pearson: Compute the Pearson correlation of a variable x with many...
row.spearman: Compute Spearmans rank-based correlation of many variables...
See all...

All man pages Function index File listing

Man pages

correlation.data: Sample ExpressionSet object of correlation.data
grenander.ebp: Grenander EBP.
GroupComp.data: Sample ExpressionSet of GroupComp.data
HybridMTest-package: A powerful tool in gene expression hypothesis testing.
hybrid.test: Hybrid Multiple Testing of Gene Expression Data
row.kgrp.shapiro: Shapiro Wilk test of normality.
row.kruskal.wallis: Apply the Kruskal-Wallis test many times
row.oneway.anova: Perform one-way ANOVA for many variables.
row.pearson: Compute the Pearson correlation of a variable x with many...
row.slr.shapiro: Test normality of residuals for many variables.
row.spearman: Compute Spearmans rank-based correlation of many variables...

Functions

GroupComp.data Man page
HybridMTest-package Man page
bartlett.test2 Source code
compute.sim.auc Source code
corr.sim Source code
corr.sim.summary Source code
correlation.data Man page
generate.corr.data Source code
generate.kgroup.data Source code
generate.surv.data Source code
get.best.pvals Source code
grenander Source code
grenander.ebp Man page Source code
hybrid.test Man page Source code
kgroup.sim Source code
kgroup.sim.summary Source code
ranksum.test Source code
row.T.test Source code
row.bartlett Source code
row.cox Source code
row.fligner Source code
row.jung Source code
row.kgrp.shapiro Man page Source code
row.kruskal.wallis Man page Source code
row.oneway.anova Man page Source code
row.pearson Man page Source code
row.ranksum Source code
row.slr.resids Source code
row.slr.shapiro Man page Source code
row.spearman Man page Source code
row.summary Source code
shapiro.test2 Source code
surv.sim Source code
surv.sim.summary Source code

Files

DESCRIPTION
NAMESPACE
R
R/bartlett.test2.R
R/compute.sim.auc.R
R/corr.sim.R
R/corr.sim.summary.R
R/generate.corr.data.R
R/generate.kgroup.data.R
R/generate.surv.data.R
R/grenander.R
R/grenander.ebp.R
R/hybrid.test.R
R/kgroup.sim.R
R/kgroup.sim.summary.R
R/ranksum.test.R
R/row.T.test.R
R/row.bartlett.R
R/row.cox.R
R/row.fligner.R
R/row.jung.R
R/row.kgrp.shapiro.R
R/row.kruskal.wallis.R
R/row.oneway.anova.R
R/row.pearson.R
R/row.ranksum.R
R/row.slr.resids.R
R/row.slr.shapiro.R
R/row.spearman.R
R/row.summary.R
R/shapiro.test2.R
R/surv.sim.R
R/surv.sim.summary.R
build
build/vignette.rds
data
data/GroupComp.data.rda
data/correlation.data.rda
inst
inst/doc
inst/doc/HybridMTest.R
inst/doc/HybridMTest.Rnw
inst/doc/HybridMTest.pdf
man
man/GroupComp.data.Rd
man/HybridMTest-package.Rd
man/correlation.data.Rd
man/grenander.ebp.Rd
man/hybrid.test.Rd
man/row.kgrp.shapiro.Rd
man/row.kruskal.wallis.Rd
man/row.oneway.anova.Rd
man/row.pearson.Rd
man/row.slr.shapiro.Rd
man/row.spearman.Rd
vignettes
vignettes/HybridMTest.Rnw
vignettes/Thumbs.db
HybridMTest documentation built on May 20, 2017, 10:05 p.m.

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