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roxygenize new version

Marta R. Hidalgo authored on 01/12/2022 13:02:29
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@@ -12,7 +12,7 @@ normalize_paths(path_vals, metaginfo)
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 \item{metaginfo}{Pathways object}
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 }
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 \value{
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-SummarizedExperiment or matrix of normalized pathway values, 
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+SummarizedExperiment or matrix of normalized pathway values,
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 depending on the class of \code{path_vals}.
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 }
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 \description{
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Debugging check problems, basically because of the SummarizedExperiment, and bumping version

Marta R. Hidalgo authored on 17/04/2019 17:47:04
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@@ -7,12 +7,13 @@
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 normalize_paths(path_vals, metaginfo)
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 }
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 \arguments{
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-\item{path_vals}{Matrix of the pathway values}
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+\item{path_vals}{SummarizedExperiment or matrix of the pathway values}
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 \item{metaginfo}{Pathways object}
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 }
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 \value{
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-Matrix of normalized pathway values
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+SummarizedExperiment or matrix of normalized pathway values, 
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+depending on the class of \code{path_vals}.
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 }
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 \description{
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 Due to the nature of the Hipathia method, the length of a pathway may
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Adding new MAN files

Marta R. Hidalgo authored on 14/02/2018 10:50:27
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new file mode 100644
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@@ -0,0 +1,34 @@
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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{normalize_paths}
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+\alias{normalize_paths}
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+\title{Normalize the pathway matrix by rows}
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+\usage{
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+normalize_paths(path_vals, metaginfo)
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+}
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+\arguments{
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+\item{path_vals}{Matrix of the pathway values}
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+
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+\item{metaginfo}{Pathways object}
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+}
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+\value{
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+Matrix of normalized pathway values
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+}
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+\description{
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+Due to the nature of the Hipathia method, the length of a pathway may
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+influence its signal rank. In order to compare signal values among
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+subpathways, we strongly recommend to normalize the matrix with this
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+normalization.
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+}
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+\details{
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+This function removes the bias caused by the length of the subpathways
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+by dividing by the value obtained from running the method with a basal
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+value of 0.5 at each node.
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+}
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+\examples{
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+data(path_vals)
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+pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
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+"hsa04012"))
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+path_normalized <- normalize_paths(path_vals, pathways)
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+
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+}