@@ -28,7 +28,7 @@ parseKGMLexpandMaps(file, downloadmethod = "auto", genesOnly = TRUE, localdir,..

   \url{https://www.genome.jp/kegg/pathway/hsa/hsa04115.html}, where p53

   signalling pathway contains other two pathways 'apoptosis' and 'cell

   cycle'. This function parses these pathways (refered as 'maps' in KGML

-  manual), download their KGML files from KEGG FTP website, parse them

+  manual), download their KGML files from KEGG REST API, parse them

   individually, and merge all the children pathway graphs with the

   parental pathway into one graph object. The graph is returned as the

   function value.

@@ -8,7 +8,7 @@

   in sequence to make expanding maps easier.

 }

 \usage{

-parseKGMLexpandMaps(file, downloadmethod = "wget", genesOnly = TRUE, localdir,...)

+parseKGMLexpandMaps(file, downloadmethod = "auto", genesOnly = TRUE, localdir,...)

 }

 %- maybe also 'usage' for other objects documented here.

 \arguments{

@@ -25,7 +25,7 @@ parseKGMLexpandMaps(file, downloadmethod = "wget", genesOnly = TRUE, localdir,..

 \details{

   In KEGG pathways there're usually pathways contained('cross-linked')

   in other pathways, for example see

-  \url{http://www.genome.jp/kegg/pathway/hsa/hsa04115.html}, where p53

+  \url{https://www.genome.jp/kegg/pathway/hsa/hsa04115.html}, where p53

   signalling pathway contains other two pathways 'apoptosis' and 'cell

   cycle'. This function parses these pathways (refered as 'maps' in KGML

   manual), download their KGML files from KEGG FTP website, parse them

@@ -42,6 +42,6 @@ parseKGMLexpandMaps(file, downloadmethod = "wget", genesOnly = TRUE, localdir,..

 \value{

   A directed graph object

 }

-\references{KGML Document manual \url{http://www.genome.jp/kegg/docs/xml/}}

+\references{KGML Document manual \url{https://www.genome.jp/kegg/docs/xml/}}

 \author{ Jitao David Zhang \url{[email protected]}}

 \seealso{ for most users it is enough to use \code{\link{parseKGML2Graph}} }

@@ -43,5 +43,5 @@ parseKGMLexpandMaps(file, downloadmethod = "wget", genesOnly = TRUE, localdir,..

   A directed graph object

 }

 \references{KGML Document manual \url{http://www.genome.jp/kegg/docs/xml/}}

-\author{ Jitao David Zhang \url{[email protected]}}

+\author{ Jitao David Zhang \url{[email protected]}}

 \seealso{ for most users it is enough to use \code{\link{parseKGML2Graph}} }

new file mode 100644

@@ -0,0 +1,47 @@

+\name{parseKGMLexpandMaps}

+\alias{parseKGMLexpandMaps}

+%- Also NEED an '\alias' for EACH other topic documented here.

+\title{ A convenient function to parse KGML and expand its containing

+  maps into one graph object }

+\description{

+  The function does several tasks implemented in the KEGGgraph package

+  in sequence to make expanding maps easier.

+}

+\usage{

+parseKGMLexpandMaps(file, downloadmethod = "wget", genesOnly = TRUE, localdir,...)

+}

+%- maybe also 'usage' for other objects documented here.

+\arguments{

+  \item{file}{ A KGML file }

+  \item{downloadmethod}{ passed to \code{\link{download.file}} function

+    as 'method', see its documentation for more details }

+  \item{genesOnly}{ logical, should only the genes nodes remain in the

+    returned graph object? }

+  \item{localdir}{ character string, if specified, the function tries to

+    read files with the same base name from a local directory, useful

+    when there are file copies on the client.}

+  \item{\dots}{ Other parameters passed to  \code{\link{download.file}} }

+}

+\details{

+  In KEGG pathways there're usually pathways contained('cross-linked')

+  in other pathways, for example see

+  \url{http://www.genome.jp/kegg/pathway/hsa/hsa04115.html}, where p53

+  signalling pathway contains other two pathways 'apoptosis' and 'cell

+  cycle'. This function parses these pathways (refered as 'maps' in KGML

+  manual), download their KGML files from KEGG FTP website, parse them

+  individually, and merge all the children pathway graphs with the

+  parental pathway into one graph object. The graph is returned as the

+  function value.

+

+  Since different graphs does not have unique node identifiers unless

+  the genes are expanded, so by using this function user has to expand

+  the genes. Another disadvantage is that so far due to the

+  implementation, the KEGGnodeData and KEGGedgeData is lost during the

+  merging. This however will probably be changed in the future version.

+}

+\value{

+  A directed graph object

+}

+\references{KGML Document manual \url{http://www.genome.jp/kegg/docs/xml/}}

+\author{ Jitao David Zhang \url{[email protected]}}

+\seealso{ for most users it is enough to use \code{\link{parseKGML2Graph}} }