pathways-ReactomeAnalysisResult-method: ReactomeAnalysisResult - pathways

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

ReactomeAnalysisResult - pathways

Description

Combines and returns the pathways of all analysed datasets.

Usage

## S4 method for signature 'ReactomeAnalysisResult'
pathways(x, p = 0.01, order_by = NULL, ...)

Arguments

x	ReactomeAnalysisResult.
p	Minimum p-value to accept a pathway as significantly regulated. Default is 0.01.
order_by	Name of the dataset to sort the result list by. By default, the results are sorted based on the first dataset.
...	Additional parameters for specific implementations.

Value

A data.frame containing all merged pathways.

See Also

Other ReactomeAnalysisResult functions: get_result(), names,ReactomeAnalysisResult-method, open_reactome(), plot_correlations(), plot_gsva_heatmap(), plot_gsva_pathway(), plot_heatmap(), plot_volcano(), reactome_links(), result_types()

Examples

# load an example result
library(ReactomeGSA.data)
data(griss_melanoma_result)

# get the combined pathway result
pathway_result <- pathways(griss_melanoma_result)

head(pathway_result)

reactome/ReactomeGSA documentation built on Nov. 9, 2024, 10:56 a.m.