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 summary.
eX:
Object of class "matrix". The transformed data matrix.
genesets:
A list of vectors indicating the tested genes.
IminH:
Object of class "matrix". Needed when drawing the various diagnostic plots.
fit:
Object of class "list". This list contains one element which is of class "lm", "glm", "coxph" or "coxph.null". Thhis latter object contains the fitted model of the null hypothesis.
PermQs:
Object of class "matrix". Stores the permuted test statistics generated by a call to permutations.
SamplingZs:
Object of class "list". Stores the standardized test statistics of random gene sets generated by a call to sampling.

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.
size
(gt.result): Extracts a vector with the number of genes tested for each pathway.
p.value
(gt.result): Extracts the p-values.
z.score
(gt.result): Extracts z-score (Q - EQ) / sd(Q).
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.
combine
(gt.result): Combines two {gt.result} objects to one, provided the data and model match.
fit
(gt.result): Extracts the fitted (adjust)model.
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 4.12.0 Index]