ReactomeAnalysisRequest {ReactomeGSA} | R Documentation |
This class is used to collect all information required to submit an analysis request to the Reactome Analysis System.
ReactomeAnalysisRequest(method)
method |
character. Name of the method to use. |
A ReactomeAnalysisRequest object.
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
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