ReactomeAnalysisResult-class {ReactomeGSA} | R Documentation |
A ReactomeAnalysisResult object contains the pathway analysis results of all submitted datasets at once.
This class represents a result retrieved from the Reactome Analysis Service. It is returned
by get_reactome_analysis_result
and its wrapper perform_reactome_analysis
.
Generally, object of this class should not be created manually.
A ReactomeAnalysisResult object.
reactome_release
The Reactome version used to create this result.
mappings
Stores the mapping results that were generated for this analysis.
results
A named list containing the actual analysis results for every dataset and possibly combined results as well.
reactome_links
Links pointing to reactome results as a list.
names
:
Retrieves the names of all datasets in the result object
result_types
:
Retrieves the available result types
pathways
:
Merges the pathway results of all analysed datasets.
get_result
:
Retrieve a specific result as data.frame
reactome_links
:
Displays / retrieves the URLs to the available visualizations in Reactome's pathway browser.
open_reactome
:
Opens the specified Reactome visualization in the system's default browser.
# load an example result object library(ReactomeGSA.data) data(griss_melanoma_result) # retrieve the names of all datasets in the result names(griss_melanoma_result) # get the combined pathway result pathway_result <- pathways(griss_melanoma_result) # check which result types are available result_types(griss_melanoma_result) # get the fold changes for the first dataset first_dataset_name <- names(griss_melanoma_result)[1] first_fc <- get_result(griss_melanoma_result, "fold_changes", first_dataset_name)