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]