gt.result-class {globaltest} | R Documentation |

The class gt.result is the output of a call to
`globaltest`

and the input of various plotting
functions to visualize the test result.

`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.

- 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`

.

Jelle Goeman: j.j.goeman@lumc.nl; Jan Oosting

`globaltest`

, `sampleplot`

,
`geneplot`

, `permutations`

.

[Package *globaltest* version 3.2.0 Index]