SubramanianTest-class: PRIVATE class : An S4 class to represent a ranked based tests...

In koralgooll/MulEA: MulEA - A Tool for Multi Enrichment Analysis

PRIVATE class : An S4 class to represent a ranked based tests in Mulea.

Description

PRIVATE class : An S4 class to represent a ranked based tests in Mulea.

Usage

## S4 method for signature 'SubramanianTest'
run_test(model)

Arguments

model

Object of s4 class represents Mulea Test.

Value

dataframe with presented columns 'ontologyId', 'ontologyName', 'nrCommonGenesOntologySet', 'nrCommonGenesOntologyBackground', 'pValue', 'adjustedPValue'

run_test method for SubramanianTest object. Used as private function.

Methods (by generic)

• run_test(SubramanianTest): runs test calculations.

Slots

gmt

A data.frame representing GMT's reprezentation of model.

element_names

A data from expeciment to analize accross model.

element_scores

A vectore of element_scores per element_names.

p

A power of weight.

element_score_type

Defines the GSEA score type. Only positive element_scores - "pos", only negative element_scores - "neg" and mixed (standard) - "std".

Examples

## Not run: 
#It is a private s4 object. Look at GSAE's examples.

## End(Not run)
## Not run: 
#It is a private method. Look at run_test of GSEA's examples.

## End(Not run)

koralgooll/MulEA documentation built on Nov. 23, 2023, 3:27 p.m.