man/normalize_paths.Rd
 37821d35  % 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{  8eb08e9d  \item{path_vals}{SummarizedExperiment or matrix of the pathway values}  37821d35  \item{metaginfo}{Pathways object} } \value{  f4adf001  SummarizedExperiment or matrix of normalized pathway values,  8eb08e9d  depending on the class of \code{path_vals}.  37821d35  } \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) }