Description Slots Note Author(s) See Also

This class represents the results of the unified Wilcoxon-Mann-Whitney test. It contains all necessary information for the vulcano and forest plots. For this class a number of methods is foreseen, among which accessors for every slot.

`type`

:object of class

`"character"`

, containing the type of analysis (either H or O, see`uWMW`

for more details.)`housekeeping`

:object of class

`"character"`

, containing either NULL or the names of the housekeeping features used in the HME version of`uWMW`

.`names`

:object of class

`"character"`

, containing the names of the features that were used in the test.`logOR`

:object of class

`"numeric"`

, containing the estimated log odds ratios from the uWMW test.`se`

:object of class

`"numeric"`

, containing the standard errors on the estimated log odds ratios.`OR`

:object of class

`"numeric"`

, containing the odds ratios estimated by the uWMW test. This slot is accessed using the function`oddsRatio()`

`z.value`

:object of class

`"numeric"`

, containing the Z values related to the odds ratios estimated by the uWMW test. These z-values relate to the chance that a specific feature is up- or downregulated, and are used as the basis for determining the p values.`p.value`

:object of class

`"numeric"`

, containing the p values related to the odds ratios estimated by the uWMW test. These p-values relate to the chance that a specific feature is up- or downregulated.`coef`

:object of class

`"numeric"`

, containing the estimated coefficient of the PIM model that's used in the uWMW test.`vcov`

:matrix of class

`"numeric"`

, containing the variance-covariance matrix related to the estimated coefficients.`id`

:vector of class

`"numeric"`

, containing the sorting order of the features. This slot is set using the function`sort`

`orderedBy`

:character value, indicating whether the object contains an order and if so, based on which slot. Possible values are "none", "p", "z", "or", "se" or "name". Defaults to "none".

`groupinfo`

:character vector of length 2, indicating the groups. This slot is mainly used to show how the probabilistic indices are calculated.

For this class, `show`

and `length`

methods are defined. `length`

will give you the number of features.

Joris Meys

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