SOUP (version 1.1)

PermSpace: Class PermSpace

Description

Permutation Space

Methods for function plot in package SOUP

Objects from the Class

Objects can be created by calls of the form new("PermSpace", ...). It contains information of permutation spaces used in the analysis, the combined test statistics and p-values, IDs (row indexes) and the seed for the RNG, the rawStats (non-combined test statistics) and comb.funct (the nonparametric combining function). But objects of the class are principally supposed to be created and used internally for storing results of SOUP.

Slots

seed:

integer seed for the Random Number Generator

T.H0Low:

matrix containing the permutation space of combined test statistics with null hypothesis $H_0: x_i <= x_h$,="" $i="" <="" h$,="" $i,h="1,\ldots,G$

T.H0Gre:

matrix containing the permutation space of combined test statistics with null hypothesis $H_0: x_i <= x_h$,="" $i="" <="" h$,="" $i,h="1,\ldots,G$

P.H0Low:

matrix containing the permutation space of combined p-values with null hypothesis $H_0: x_i <= x_h$,="" $i="" <="" h$,="" $i,h="1,\ldots,G$

P.H0Gre:

matrix containing the permutation space of combined p-values with null hypothesis $H_0: x_i <= x_h$,="" $i="" <="" h$,="" $i,h="1,\ldots,G$

IDs:

matrix permutation space of row indexes

rawStats:

$3$-way array containing the permutation space of non-combined test statistics

comb.funct:

nonparametric combining function used for NPC of rawStats

Methods

initialize

constructor used when calling new(PermSpace, ...)

show

signature(object = "PermSpace"): shows only the main information (on screen) for the object

print

signature(x = "PermSpace"): It prints the whole object on screen (mostly useful for external saving)

signature(x = "PermSpace")

Plots a bivariate representation of the permutation space, when there are more than $2$ (original) variables then a Principal Component Analysis is performed and the first $2$ variables in the transformed space are shown

Details

Contains the permutation space of the test statistic, useful for reproducibility of the analyses

Examples

showClass("PermSpace")