man/get_paths_data.Rd
37821d35
 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/utils.R
8bf512f4
 \name{get_paths_data}
 \alias{get_paths_data}
 \title{Gets the object of subpathway activation values}
37821d35
 \usage{
8bf512f4
 get_paths_data(results, matrix = FALSE)
37821d35
 }
 \arguments{
 \item{results}{Results object as returned by \code{hipathia}.}
8bf512f4
 
f4adf001
 \item{matrix}{Boolean, if TRUE the function returns a matrix object, if
8bf512f4
 FALSE (as default) returns a SummarizedExperiment object.}
37821d35
 }
 \value{
f4adf001
 Object, either a SummarizedExperiment or a matrix, with the levels
8bf512f4
 of activation of each decomposed subpathway for each sample.
37821d35
 }
 \description{
8bf512f4
 This function returns the object with the levels of activation of each
37821d35
 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 \code{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.
 }
 \examples{
 data(results)
8bf512f4
 path_vals <- get_paths_data(results)
37821d35
 
 }