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 result.

Slots

res:
Object of class "matrix". Test results, with a row for each element of test.genes, and the following columns: path.n: length of input vector, test.n: number of rows in X that matched the input vector, Q: test statistic, EQ: expectation for the test statistic, seQ: standard deviation of the test statistic, p.val: p value comp.p: comparative p (after a call to sampling).
X:
Object of class "matrix". The transformed data matrix.
Y:
Object of class "numeric". The transformed clinical outcome vector.
test.genes:
A list of vectors indicating the tested genes.
IminH:
Object of class "matrix". Needed when drawing the various diagnostic plots.
pars:
Object of class "matrix". Contains estimates of parameters of the null model.
Rsquare:
Object of class "numeric". Percentage of the variance of Y left after adjustment for confounders or known risk factors.
Qs:
Object of class "matrix". Contains the permuted test statistics generated by the permutations method.
model:
Object of class "character". The model used by the test ("linear", "logistic" or "survival").
adjustmodel:
Object of class "formula". The model used when adjusting.
levels:
Object of class "vector". The group labels tested (logistic model only).
df.adjust:
Object of class "numeric". The number of degrees of freedom used in the adjustment of the test.

Methods

show
(gt.result): Summarizes the test result.
"["
(gt.result): Extracts results of one or more pathways if multiple pathways were tested.
length
(gt.result): The number of pathways tested.
p.value
(gt.result): Extracts the p-values.
sort
(gt.result): Sorts the pathways to increasing p-values.
result
(gt.result): Extracts the results matrix.
names
(gt.result): Extracts the pathway names.
names<-
(gt.result): Changes the pathway names.
hist
(gt.result): Produces a histogram to visualize the permutations generated by permutations.
geneplot
(gt.result): The geneplot produces a plot to show the influence of individual genes on the test result produced by globaltest.
sampleplot
(gt.result): The sampleplot produces a plot to show the influence of individual samples on the test result produced by globaltest.
permutations
(gt.result): The function permutations recalculates the p-values using permutations of the outcome Y.
sampling
(gt.result): The function sampling compares the p-values with p-values of randomly generated pathways.
checkerboard
(gt.result): Produces a plot to visualize the test result produced by globaltest by showing the association between pairs of samples.
regressionplot
(gt.result): 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; Jan Oosting

See Also

globaltest, sampleplot, geneplot, permutations.


[Package globaltest version 3.2.0 Index]