perform_reactome_analysis {ReactomeGSA} | R Documentation |
This function wraps all steps required to perform
an Analysis using the Reactome Analysis Service. It submits
the passed ReactomeAnalysisRequest
object to the
Reactome Analysis Service API, checks the submitted analysis'
status and returns the result once the analysis is complete.
perform_reactome_analysis( request, verbose = TRUE, compress = TRUE, reactome_url = NULL )
request |
|
verbose |
logical. If |
compress |
logical. If |
reactome_url |
URL of the Reactome API Server. Overwrites the URL set in the 'reactome_gsa.url' option. Specific ports can be set using the standard URL specification (for example http://your.service:1234) |
The analysis' result
# create a request using Camera as an analysis library(ReactomeGSA.data) data(griss_melanoma_proteomics) my_request <- ReactomeAnalysisRequest(method = "Camera") # set maximum missing values to 0.5 and do not create any reactome visualizations my_request <- set_parameters(request = my_request, max_missing_values = 0.5, create_reactome_visualization = FALSE) # add the dataset my_request <- add_dataset(request = my_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")) # perform the analysis my_result <- perform_reactome_analysis(request = my_request, verbose = FALSE)