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Question: Change enzyme code (EC) into gene symbol
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gravatar for Luo Weijun
4.3 years ago by
Luo Weijun1.4k
United States
Luo Weijun1.4k wrote:
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
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