ReactomeAnalysisRequest: ReactomeAnalysisRequest class

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

ReactomeAnalysisRequest class

Description

This class is used to collect all information required to submit an analysis request to the Reactome Analysis System.

Usage

ReactomeAnalysisRequest(method)

ReactomeAnalysisRequest(method)

Arguments

method

character. Name of the method to use.

Value

A ReactomeAnalysisRequest object.

Slots

method

character. Name of the method to use

request_object

list. This slot should not be set manually. It stores the internal request representation and should be modified using the classes' functions. To add parameters, use set_parameters,ReactomeAnalysisRequest-method

Examples

library(ReactomeGSA.data)
library(methods)

# create the request method and specify its method
request <- ReactomeAnalysisRequest(method = "Camera")

# add a dataset to the request
data(griss_melanoma_proteomics)

request <- add_dataset(request = request,
             expression_values = griss_melanoma_proteomics,
             name = "Proteomics",
             type = "proteomics_int",
             comparison_factor = "condition",
             comparison_group_1 = "MOCK",
             comparison_group_2 = "MCM",
             additional_factors = c("cell.type", "patient.id"))

# to launch the actual analysis use the perform_reactome_analysis function

reactome/ReactomeGSA documentation built on Nov. 13, 2023, 11:13 p.m.