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  }