#### roxygenize new version

Marta R. Hidalgo authored on 01/12/2022 13:02:29
Showing1 changed files
 ... ... @@ -9,11 +9,11 @@ get_paths_data(results, matrix = FALSE) 9 9  \arguments{ 10 10  \item{results}{Results object as returned by \code{hipathia}.} 11 11   12 -\item{matrix}{Boolean, if TRUE the function returns a matrix object, if  12 +\item{matrix}{Boolean, if TRUE the function returns a matrix object, if 13 13  FALSE (as default) returns a SummarizedExperiment object.} 14 14  } 15 15  \value{ 16 -Object, either a SummarizedExperiment or a matrix, with the levels  16 +Object, either a SummarizedExperiment or a matrix, with the levels 17 17  of activation of each decomposed subpathway for each sample. 18 18  } 19 19  \description{

#### Adapting hipathia to SummarizedExperiment and MultiAssayExperiment objects

Marta R. Hidalgo authored on 05/03/2018 15:56:13
Showing1 changed files
 1 1 new file mode 100644 ... ... @@ -0,0 +1,44 @@ 1 +% Generated by roxygen2: do not edit by hand 2 +% Please edit documentation in R/utils.R 3 +\name{get_paths_data} 4 +\alias{get_paths_data} 5 +\title{Gets the object of subpathway activation values} 6 +\usage{ 7 +get_paths_data(results, matrix = FALSE) 8 +} 9 +\arguments{ 10 +\item{results}{Results object as returned by \code{hipathia}.} 11 + 12 +\item{matrix}{Boolean, if TRUE the function returns a matrix object, if  13 +FALSE (as default) returns a SummarizedExperiment object.} 14 +} 15 +\value{ 16 +Object, either a SummarizedExperiment or a matrix, with the levels  17 +of activation of each decomposed subpathway for each sample. 18 +} 19 +\description{ 20 +This function returns the object with the levels of activation of each 21 +subpathway for each sample. Rows represent the subpathways and columns 22 +represent the samples. Each cell is the value of activation of a subpathway 23 +in a sample. 24 + 25 +Rownames are the IDs of the subpathways. In order to transform IDs into 26 +readable names, use \code{get_path_names}. 27 + 28 +Effector subpathways are subgraphs of a pathway including all the paths 29 +leading to an effector protein. Effector proteins are defined as final 30 +nodes in the graph. Each effector protein (final node) in a pathway 31 +defines its own effector subpathway as the nodes and edges in a path leading 32 +to it. 33 + 34 +Decomposed subpathways are subgraphs of a pathway including all the paths 35 +starting in a receptor protein and ending in an effector protein. Receptor 36 +proteins are defined as initial nodes and effector proteins are defined 37 +as final nodes in the graph. Each effector subpathway can be decomposed 38 +in as many decomposed subpathways as initial nodes it includes. 39 +} 40 +\examples{ 41 +data(results) 42 +path_vals <- get_paths_data(results) 43 + 44 +}