perform_reactome_analysis: Perform a Reactome Analaysis

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

Description

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.

Usage

perform_reactome_analysis(
  request,
  verbose = TRUE,
  compress = TRUE,
  reactome_url = NULL
)

Arguments

request	ReactomeAnalysisRequest to submit.
verbose	logical. If FALSE status messages are not printed to the console.
compress	logical. If TRUE (default) the request data is compressed before submitting it to the ReactomeGSA API. This is the generally recommended way and should only be disabled for debugging purposes.
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)

Value

The analysis' result

Examples

# 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)

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