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


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Documentation for package ‘globaltest’ version 5.10.0

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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