get_paths_data: Gets the object of subpathway activation values

In babelomics/hipathia: HiPathia: High-throughput Pathway Analysis

Gets the object of subpathway activation values

Description

This function returns the object with the levels of activation of each subpathway for each sample. Rows represent the subpathways and columns represent the samples. Each cell is the value of activation of a subpathway in a sample.

Rownames are the IDs of the subpathways. In order to transform IDs into readable names, use get_path_names.

Effector subpathways are subgraphs of a pathway including all the paths leading to an effector protein. Effector proteins are defined as final nodes in the graph. Each effector protein (final node) in a pathway defines its own effector subpathway as the nodes and edges in a path leading to it.

Decomposed subpathways are subgraphs of a pathway including all the paths starting in a receptor protein and ending in an effector protein. Receptor proteins are defined as initial nodes and effector proteins are defined as final nodes in the graph. Each effector subpathway can be decomposed in as many decomposed subpathways as initial nodes it includes.

Usage

get_paths_data(results, matrix = FALSE)

Arguments

results	Results object as returned by hipathia.
matrix	Boolean, if TRUE the function returns a matrix object, if FALSE (as default) returns a SummarizedExperiment object.

Value

Object, either a SummarizedExperiment or a matrix, with the levels of activation of each decomposed subpathway for each sample.

Examples

data(results)
path_vals <- get_paths_data(results)

babelomics/hipathia documentation built on July 27, 2022, 2:23 p.m.