gsea-class: Gene Set Enrichment Analysis (GSEA)

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

Gene Set Enrichment Analysis (GSEA)

Description

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

Usage

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

Arguments

model

Object of s4 class represents Mulea Test.

Value

GSEA object. This object represents ranked based tests.

run_test method for GSEA object. Returns results of counting using methods from ranking based area.

Methods (by generic)

• run_test(gsea): runs test calculations.

Slots

gmt

A data frame which contains the data, imported from a GMT file.

element_names

A vector of elements names to include in the analysis, ordered by their scores.

element_scores

A vector of element_scores per element_names.

gsea_power

A power of weight. Default value is 1.

element_score_type

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

number_of_permutations

The number of permutations used in KS test. Default value is 1000.

test

character

Examples

modelDfFromFile <- MulEA::read_gmt(
  file = system.file(package="MulEA", "extdata", "model.gmt"))
dataFromExperiment <- c("FBgn0004407", "FBgn0010438", "FBgn0003742",
                        "FBgn0029709", "FBgn0030341", "FBgn0037044",
                        "FBgn0002887", "FBgn0028434", "FBgn0030170",
                        "FBgn0263831")
dataFromExperimentScores <- c(0.09, 0.11, 0.15, 0.20, 0.21, 0.24, 0.28, 0.30,
                              0.45, 0.50)
GSEASubramanian <- gsea(gmt = modelDfFromFile,
                        element_names = dataFromExperiment,
                        element_scores = dataFromExperimentScores)
GSEASubramanianRes <- MulEA::run_test(GSEASubramanian)

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