man/normalize_paths.Rd
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 % Generated by roxygen2: do not edit by hand
 % Please edit documentation in R/utils.R
 \name{normalize_paths}
 \alias{normalize_paths}
 \title{Normalize the pathway matrix by rows}
 \usage{
 normalize_paths(path_vals, metaginfo)
 }
 \arguments{
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 \item{path_vals}{SummarizedExperiment or matrix of the pathway values}
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 \item{metaginfo}{Pathways object}
 }
 \value{
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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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 }
 \description{
 Due to the nature of the Hipathia method, the length of a pathway may
 influence its signal rank. In order to compare signal values among
 subpathways, we strongly recommend to normalize the matrix with this
 normalization.
 }
 \details{
 This function removes the bias caused by the length of the subpathways
 by dividing by the value obtained from running the method with a basal
 value of 0.5 at each node.
 }
 \examples{
 data(path_vals)
 pathways <- load_pathways(species = "hsa", pathways_list = c("hsa03320",
 "hsa04012"))
 path_normalized <- normalize_paths(path_vals, pathways)
 
 }