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

In mulea: Enrichment Analysis using Multiple Ontologies and False Discovery Rate

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

data.frame with presented columns 'ontology_id', 'ontology_name', 'nr_common_with_tested_elements', 'p_value', 'adjusted_p_value'

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 the ontology GMT.

element_names

A vector of elements names (gene or protein names or identifiers) to include in the analysis.

element_scores

A vector of numeric values representing a score (e.g. p-value, z-score, log fold change) for each 'element_name', in the same number and order as element_name.

p

A power of weight.

element_score_type

Defines the GSEA score type.

• "pos": Only positive element_scores

• "neg": only negative element_scores - "neg" and mixed

• "std": standard – containing both positive and negative scores Default value is "std".

mulea documentation built on Sept. 30, 2024, 9:44 a.m.