uwmwRes-class: Class uwmwRes

In unifiedWMWqPCR: Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data

Description

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.

Slots

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.

Note

For this class, show and length methods are defined. length will give you the number of features.

Author(s)

Joris Meys

See Also

uwmw_Accessors

unifiedWMWqPCR documentation built on Nov. 8, 2020, 6:05 p.m.