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
.