% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/utils.R
\title{Loads the pathways object.}
load_pathways(species, pathways_list = NULL)
\item{species}{Species of the samples.}

\item{pathways_list}{Vector of the IDs of the pathways to load. By default
all available pathways are load.}
An pathways object including
* \code{species} Species to which the pathways are related.
* \code{pathigraphs} List of Pathigraph objects. Each Pathigraph contains
the necessary information of a pathway for it to be analyzed
with \code{Hipathia}.
* \code{all_genes} List of all the genes included in the selection of
pathways stored in \code{pathigraphs}.
* \code{eff_norm} Vector of normalization values for effector subpathways.
* \code{path_norm} Vector of normalization values for decomposed
Loads the pathways object, which includes information about the pathways
to be analyzed.
The object of pathways includes information about the pathways and the
subpathways which will be analyzed. This object must be provided to some
of the functions (like \code{hipathia} or \code{quantify_terms}) in the
package. These functions will analyze all the pathways included in this
object. By default, all available pathways are load. In order to restrict
the analysis to a predefined set of pathways, specify the set of pathways
to load with the parameter \code{pathways_list}.
\dontrun{pathways <- load_pathways("hsa")   # Loads all pathways for human}
pathways <- load_pathways("mmu", c("mmu03320", "mmu04024", "mmu05200"))
   # Loads pathways 03320, 04024 and 05200 for mouse