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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/StarBioTrek@125294 bc3139a8-67e5-0310-9ffc-ced21a209358

Claudia Cava authored on 19/12/2016 16:16:46
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@@ -2,7 +2,7 @@ Package: StarBioTrek
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 Type: Package
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 Title: StarBioTrek
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 Version: 1.0.1
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-Date: 12-12-2016
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+Date: 12-19-2016
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 Author: Claudia Cava,
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     Isabella Castiglioni
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 Maintainer: Claudia Cava <claudia.cava@ibfm.cnr.it>
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/path_star.R
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+\name{matrix_plot}
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+\alias{matrix_plot}
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+\title{Get human KEGG pathway data and a gene expression matrix in order to obtain a matrix with the mean gene expression for only pathways given in input .}
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+\usage{
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+matrix_plot(DataMatrix, pathway)
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+}
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+\arguments{
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+\item{DataMatrix}{gene expression matrix (eg.TCGA data)}
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+
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+\item{pathway}{pathway data as provided by getKEGGdata}
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+}
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+\value{
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+a matrix for each pathway (mean gene expression level belong to that pathway)
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+}
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+\description{
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+GE_matrix creates a matrix of mean gene expression for pathways given by the user.
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+}
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+\examples{
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+list_path_plot<-matrix_plot(DataMatrix=tumo[,1:2],pathway=path)
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+}
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+
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+% Generated by roxygen2: do not edit by hand
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+% Please edit documentation in R/path_star.R
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+\name{path_net}
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+\alias{path_net}
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+\title{Get human KEGG pathway data and network data in order to define the common gene.}
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+\usage{
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+path_net(pathway, net_type)
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+}
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+\arguments{
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+\item{pathway}{pathway data as provided by getKEGGdata}
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+
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+\item{net_type}{network data as provided by getNETdata}
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+}
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+\value{
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+a list of network data for each pathway (interacting genes belong to that pathway)
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+}
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+\description{
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+path_net creates a list of network data for each human pathway. The network data will be generated when interacting genes belong to that pathway.
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+}
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+\examples{
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+lista_net<-path_net(pathway=path,net_type=netw)
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+}
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+