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roxygenize new version

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

Adapting hipathia to SummarizedExperiment and MultiAssayExperiment objects

Marta R. Hidalgo authored on 05/03/2018 15:56:13
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new file mode 100644
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@@ -0,0 +1,44 @@
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/utils.R
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+\name{get_paths_data}
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+\alias{get_paths_data}
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+\title{Gets the object of subpathway activation values}
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+\usage{
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+get_paths_data(results, matrix = FALSE)
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+}
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+\arguments{
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+\item{results}{Results object as returned by \code{hipathia}.}
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+
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+\item{matrix}{Boolean, if TRUE the function returns a matrix object, if 
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+FALSE (as default) returns a SummarizedExperiment object.}
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+}
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+\value{
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+Object, either a SummarizedExperiment or a matrix, with the levels 
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+of activation of each decomposed subpathway for each sample.
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+}
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+\description{
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+This function returns the object with the levels of activation of each
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+subpathway for each sample. Rows represent the subpathways and columns
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+represent the samples. Each cell is the value of activation of a subpathway
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+in a sample.
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+
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+Rownames are the IDs of the subpathways. In order to transform IDs into
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+readable names, use \code{get_path_names}.
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+
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+Effector subpathways are subgraphs of a pathway including all the paths
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+leading to an effector protein. Effector proteins are defined as final
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+nodes in the graph. Each effector protein (final node) in a pathway
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+defines its own effector subpathway as the nodes and edges in a path leading
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+to it.
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+
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+Decomposed subpathways are subgraphs of a pathway including all the paths
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+starting in a receptor protein and ending in an effector protein. Receptor
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+proteins are defined as initial nodes and effector proteins are defined
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+as final nodes in the graph. Each effector subpathway can be decomposed
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+in as many decomposed subpathways as initial nodes it includes.
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+}
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+\examples{
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+data(results)
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+path_vals <- get_paths_data(results)
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+
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+}