ReactomeAnalysisResult-class: ReactomeAnalysisResult class

In ReactomeGSA: Client for the Reactome Analysis Service for comparative multi-omics gene set analysis

Description

A ReactomeAnalysisResult object contains the pathway analysis results of all submitted datasets at once.

Details

This class represents a result retrieved from the Reactome Analysis Service. It is returned by get_reactome_analysis_result and its wrapper perform_reactome_analysis. Generally, object of this class should not be created manually.

Value

A ReactomeAnalysisResult object.

Slots

reactome_release

The Reactome version used to create this result.

mappings

Stores the mapping results that were generated for this analysis.

results

A named list containing the actual analysis results for every dataset and possibly combined results as well.

reactome_links

Links pointing to reactome results as a list.

Methods

names: Retrieves the names of all datasets in the result object

result_types: Retrieves the available result types

pathways: Merges the pathway results of all analysed datasets.

get_result: Retrieve a specific result as data.frame

reactome_links: Displays / retrieves the URLs to the available visualizations in Reactome's pathway browser.

open_reactome: Opens the specified Reactome visualization in the system's default browser.

Examples

# load an example result object
library(ReactomeGSA.data)
data(griss_melanoma_result)

# retrieve the names of all datasets in the result
names(griss_melanoma_result)

# get the combined pathway result
pathway_result <- pathways(griss_melanoma_result)

# check which result types are available
result_types(griss_melanoma_result)

# get the fold changes for the first dataset
first_dataset_name <- names(griss_melanoma_result)[1]

first_fc <- get_result(griss_melanoma_result, "fold_changes", first_dataset_name)

ReactomeGSA documentation built on April 17, 2021, 6:01 p.m.