gt.result-class {globaltest}R Documentation

Class gt.result, for results of the function globaltest

Description

The class gt.result is the output of a call to globaltest and the input of various plotting functions to visualize the test reult.

Slots

Q
The test statistic.
EQ
The expected value of Q under the null hypothesis.
seQ
The standard deviation of Q under the null hypothesis.
p.value
The p-value resulting from the test.
Qs
Values of Q for permutations of the clinical variable
matrixR
The covariance matrix between the expression patterns of the samples.
Y
The centered clinical variable.
influence
The influence of each gene on the test statistic.
exp.influence
The expected influence of each gene on the test statistic under the null hypothesis.
test.genes
A logical vector indicating which genes were to be tested.

Methods

show
Summarizes the test result
checkerboard
Produces a plot to visualize the test result produced by globaltest by showing the association between pairs of samples.
geneplot
Produces a plot to show the influence of individual genes on the test result produced by globaltest.
permutations
Produces a histogram for visualization of the permutations used in globaltest.
regressionplot
Produces a plot which can be used to visualize the effect of specific samples on the test result produced by globaltest.

Author(s)

Jelle Goeman: j.j.goeman@lumc.nl

See Also

globaltest, regressionplot, geneplot, permutations, checkerboard.


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