[BioC] Change enzyme code (EC) into gene symbol

[Luo Weijun]

Hi Weiwei,
By default pathview sum up the gene (or compound etc) data mapped to one node, which works well in common conditions. But you may specify other methods, like taking mean, median, max etc of these mapped gene data. Check the help information within R with the following lines:
library(pathview)
?pathview
Look under argument “node.sum”.
And look on argument node.sum. page 6 of the pathview vignette gives more info on this.
Weijun

--------------------------------------------
On Sat, 8/31/13, Nick <edforum at gmail.com> wrote:

 Subject: Re: Change enzyme code (EC) into gene symbol

 Cc: "BioC Help" <bioconductor at r-project.org>
 Date: Saturday, August 31, 2013, 4:32 PM

 Hi
 I think I figured that out by
 setting kegg.native = T, same.layer = F; Oops, I think I
 just did not understand your email very well :(
 Thanks a lot!

 But one more question, how do you treat multiple
 isoforms of an enzyme for one EC code in the
 package?
 Weiwei



 On Sat, Aug 31, 2013 at 4:12 PM, Nick <edforum at gmail.com>
 wrote:

 Can I use gene symbol but keep a native KEGG
 view? I mean, I just want to replace the EC code with gene
 symbol without changing the layout or view of KEGG
 pathway?
 Thanks,


 weiwei


 On Thu, Aug 29, 2013

 wrote:


 Hi
 Weiwei,

 Yes, you can get gene symbol instead of EC (or original KEGG
 node labels). If you want a native KEGG view, set
 kegg.native = T, same.layer = F when you call pathview
 function. Otherwise, simply set set kegg.native = F for a
 Graphviz view.



 Notice that you can only modify mappable gene nodes which
 are present in the KEGG xml file as gene nodes (rather than
 KO nodes) if you work with a particular species like human
 or hsa. You may have access to all Enzyme/gene nodes if you
 work with KO pathways (species="ko").



 As example outputs, you may compare the gene symbols in
 Figure 1b and Figure 2 vs Figure 1a in the vignette. HTH.

 Weijun



 --------------------------------------------

 On Tue, 8/27/13, Nick <edforum at gmail.com>
 wrote:



  Subject: Change enzyme code (EC) into gene symbol



  Cc: "BioC Help" <bioconductor at r-project.org>

  Date: Tuesday, August 27, 2013, 8:36 PM



  Hi there,

  I am wondering if you can change the ECs for each

  enzyme on the kegg graph like pyrimidine metabolism into

  gene symbol, for example?

  thanks,



  Weiwei