Marta R. Hidalgo authored on 01/12/2022 13:02:29 | ... | ... |
@@ -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{
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Marta R. Hidalgo authored on 05/03/2018 15:56:13 | 1 | 1 |
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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+} |