get_reactome_methods: get_reactome_methods

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

get_reactome_methods

Description

Returns all available analysis methods from the Reactome analysis service.

Usage

get_reactome_methods(
  print_methods = TRUE,
  print_details = FALSE,
  return_result = FALSE,
  method = NULL,
  reactome_url = NULL
)

Arguments

print_methods	If set to TRUE (default) a (relatively) nice formatted version of the result is printed.
print_details	If set to TRUE detailed information about every method, including available parameters and description are displayed. This does not affect the data returned if return_result is TRUE.
return_result	If set to TRUE, the result is returned as a data.frame (see below)
method	If set to a method's id, only information for this method will be shown. This is especially useful if detailed information about a single method should be retrieved. This does not affect the data returned if return_result is TRUE.
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

Every method has a type, a scope, and sometimes a list of allowed values. The type (string, int = integer, float) define the expected data type. The scope defines at what level the parameter can be set. dataset level parameters can be set at the dataset level (using the add_dataset function) or at the analysis request level (using set_parameters). If these parameters are set at the analysis request level, this overwrites the default value for all datasets. analysis and global level parameters must only be set at the analysis request level using set_parameters. The difference between these two types of parameters is that while analysis parameters influence the results, global parameters only influence the behaviour of the analysis system (for example whether a Reactome visualization is created).

Value

If return_result is set to TRUE, a data.frame with one row per method. Each method has a name, description, and (optional) a list of parameters. Parameters again have a name, type, and description.

Author(s)

Johannes Griss

See Also

Other Reactome Service functions: get_reactome_data_types()

Examples

# retrieve the available methods only in an object
available_methods <- get_reactome_methods(print_methods = FALSE, return_result = TRUE)

# print all method names
available_methods$name

# list all parameters for the first method
first_method_parameters <- available_methods[1, "parameters"]
first_method_parameters

# simply print the available methods
get_reactome_methods()

# get the details for PADOG
get_reactome_methods(print_details = TRUE, method = "PADOG")

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