# Testing groups of covariates/features for association with a response variable, with applications to gene set testing

## Documentation for package ‘globaltest’ version 5.8.1

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## Help Pages

A B C D E F G H I L M N P R S V W Z misc

## -- A --

alias-method | Class "gt.object" for storing the result of the function gt
alias<- | Class "gt.object" for storing the result of the function gt
alias<--method | Class "gt.object" for storing the result of the function gt
annotation.vandeVijver | Some selected annotations for the breast cancer data from Rosetta Inpharmatics LLC and Netherlands Cancer Institute, to serve as example data in the globaltest package. (Deprecated)

## -- B --

bbase | Goodness of fit testing in regression models using Global Test
btensor | Goodness of fit testing in regression models using Global Test

## -- C --

checkerboard | Checkerboard plot for Global Test (Deprecated)
coefficients-method | Multinomial Logistic Regression
combine-method | Class "gt.result" for results of the function globaltest (Deprecated)
comparative | Comparative proportions for the Global Test
covariates | Global Test diagnostic plots

## -- D --

diagnostics | Global Test diagnostic plots
draw | Multiple testing correction for the Global Test

## -- E --

extract | Class "gt.object" for storing the result of the function gt
extract-method | Class "gt.object" for storing the result of the function gt

## -- F --

features | Global Test diagnostic plots
findFocus | Multiple testing correction for the Global Test
fit | Class "gt.result" for results of the function globaltest (Deprecated)
fit-method | Class "gt.result" for results of the function globaltest (Deprecated)
fitted.values-method | Multinomial Logistic Regression
focusLevel | Multiple testing correction for the Global Test

## -- G --

geneplot | Gene Plot for Global Test (Deprecated)
genesets | Class "gt.result" for results of the function globaltest (Deprecated)
genesets-method | Class "GOstructure" (Deprecated)
getFocus | Multiple testing on the GO graph (Deprecated)
globaltest | Global Test (Deprecated)
GOstructure | Class "GOstructure" (Deprecated)
GOstructure-class | Class "GOstructure" (Deprecated)
gt | Global Test (new implementation, 2009)
gt.barplot | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)
gt.barplot-class | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)
gt.multtest | Correct globaltest results for multiple testing (Deprecated)
gt.object | Class "gt.object" for storing the result of the function gt
gt.object-class | Class "gt.object" for storing the result of the function gt
gt.options | Options for globaltest package
gt.result | Class "gt.result" for results of the function globaltest (Deprecated)
gt.result-class | Class "gt.result" for results of the function globaltest (Deprecated)
gtBroad | Gene set testing of gene set databases using Global Test
gtConcept | Gene set testing of gene set databases using Global Test
gtGO | Gene set testing of gene set databases using Global Test
gtKEGG | Gene set testing of gene set databases using Global Test
gtKS | Goodness of fit testing in regression models using Global Test
gtLI | Goodness of fit testing in regression models using Global Test
gtPS | Goodness of fit testing in regression models using Global Test

## -- H --

hist-method | Class "gt.object" for storing the result of the function gt
hist-method | Class "gt.result" for results of the function globaltest (Deprecated)

## -- I --

inheritance | Multiple testing correction for the Global Test

## -- L --

leafNodes | Multiple testing correction for the Global Test
length-method | Class "gt.object" for storing the result of the function gt
length-method | Class "GOstructure" (Deprecated)
length-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)
length-method | Class "gt.result" for results of the function globaltest (Deprecated)

## -- M --

makeGOstructure | Multiple testing on the GO graph (Deprecated)
mlogit | Multinomial Logistic Regression
mlogit-class | Multinomial Logistic Regression
model.matrix-method | Class "gt.object" for storing the result of the function gt

## -- N --

names-method | Class "gt.object" for storing the result of the function gt
names-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)
names-method | Class "gt.result" for results of the function globaltest (Deprecated)
names<--method | Class "gt.object" for storing the result of the function gt
names<--method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)
names<--method | Class "gt.result" for results of the function globaltest (Deprecated)

## -- P --

p.adjust-method | Class "gt.object" for storing the result of the function gt
p.value | Class "gt.object" for storing the result of the function gt
p.value-method | Class "gt.object" for storing the result of the function gt
p.value-method | Class "gt.result" for results of the function globaltest (Deprecated)
permutations | Permutations version of the Global Test (Deprecated)
plot-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)

## -- R --

regressionplot | Regression Plot for Global Test (Deprecated)
reparamZ | Goodness of fit testing in regression models using Global Test
residuals-method | Multinomial Logistic Regression
result | Class "gt.object" for storing the result of the function gt
result-method | Class "gt.object" for storing the result of the function gt
result-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)
result-method | Class "gt.result" for results of the function globaltest (Deprecated)
reweighZ | Goodness of fit testing in regression models using Global Test

## -- S --

sampleplot | Sample Plot for Global Test (Deprecated)
sampling | Sampling random 'pathways' for the Global Test
scale-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)
show-method | Class "gt.object" for storing the result of the function gt
show-method | Multinomial Logistic Regression
show-method | Class "GOstructure" (Deprecated)
show-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)
show-method | Class "gt.result" for results of the function globaltest (Deprecated)
size | Class "gt.object" for storing the result of the function gt
size-method | Class "gt.object" for storing the result of the function gt
size-method | Class "gt.result" for results of the function globaltest (Deprecated)
sort-method | Class "gt.object" for storing the result of the function gt
sort-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)
sort-method | Class "gt.result" for results of the function globaltest (Deprecated)
sterms | Goodness of fit testing in regression models using Global Test
sterms-method | Class "gt.object" for storing the result of the function gt
subjects | Global Test diagnostic plots
subsets | Class "gt.object" for storing the result of the function gt
subsets-method | Class "gt.object" for storing the result of the function gt
summary-method | Class "gt.object" for storing the result of the function gt
summary-method | Multinomial Logistic Regression

## -- V --

vandeVijver | A subset of the Breast cancer data from Rosetta Inpharmatics LLC and Netherlands Cancer Institute. (Deprecated)

## -- W --

weights-method | Class "gt.object" for storing the result of the function gt

## -- Z --

z.score | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)
z.score-method | Class "gt.object" for storing the result of the function gt
z.score-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)
z.score-method | Class "gt.result" for results of the function globaltest (Deprecated)

## -- misc --

[-method | Class "gt.object" for storing the result of the function gt
[-method | Class "gt.barplot" for results of the functions geneplot and sampleplot (Deprecated)
[-method | Class "gt.result" for results of the function globaltest (Deprecated)
[[-method | Class "gt.object" for storing the result of the function gt