start_reactome_analysis: Start Reactome Analysis

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

Start Reactome Analysis

Description

Submits a ReactomeAnalysisRequest to the Reactome Analysis Service API and returns the analysis id of the submitted job.

Usage

start_reactome_analysis(request, compress = TRUE, reactome_url = NULL)

Arguments

request	ReactomeAnalysisRequest object to submit.
compress	If set (default) the JSON request data is compressed using gzip.
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)

Details

This function should only be used for very large requests that likely take a long time to complete. By default, users should use the perform_reactome_analysis function to run an analysis.

Value

character The analysis job's id.

#' @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")) # start the analysis analysis_id <- start_reactome_analysis(my_request)

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