set_parameters: set_parameters

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

set_parameters

Description

Sets the analysis parameters for the given ReactomeAnalysisRequest. If the parameter is already set, it is overwritten. Use get_reactome_methods to get a list of all available parameters for each available method.

Usage

set_parameters(request, ...)

Arguments

request	The ReactomeAnalysisRequest to set the parameters for.
...	Any name / value pair to set a parameter (see example). For a complete list of available parameters use get_reactome_methods

Details

Both, parameters with the scope "dataset" as well as "analysis" can be set on the analysis level. In this case, these parameters overwrite the system's default values. If a parameter with the scope "dataset" is defined again at the dataset level, this value will overwrite the analysis' scope value for the given dataset.

Value

The modified ReactomeAnalysisRequest object

Examples

library(methods)

# create a request object
request <- ReactomeAnalysisRequest(method = "Camera")

# add a parameter
request <- set_parameters(request, max_missing_values = 0.5, discrete_norm_function = "TMM")

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