[BioC] Pathview with non-KEGG organisms?

[Luo Weijun]

Hi Iain,
Yes, pathview can work with your problem. First map your genes to KEGG Orthology, and retrieve the KEGG ortholog IDs (gene IDs in the format of Kxxxxx) (as you have done). Just label your genes use these KEGG ortholog IDs (instead of Entrez Gene IDs or gene symbols). Then supply your data as gene.data, and set species="ko" when calling pathview function. Otherwise it would be the same as working with KEGG species data. Please check the help info for pathview function within R:
?pathview
And look on the Arguments section (gene.data, species) and Details section.

Pathview also can be used directly to visualize metagenomic or microbiome data when the data are mapped to KEGG ortholog IDs. In fact, pathview can visualize various types of molecular data as long as the data can be mapped onto pathways. Pathview automatically maps common gene/protein/compound IDs to KEGG molecular IDs for common species. For less used IDs or other species, pathview will also work if the user provides the ID mapping manually. Please check page 13-14 in the package vignette for pathview’s ID mapping functions and solutions. HTH.
Weijun

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On Fri, 7/26/13, Iain wrote:

 Subject: Pathview with non-KEGG organisms?

 Date: Friday, July 26, 2013, 1:42 AM

 Hey Weijun,

 I've been
 looking for tools that allow RNA-seq data to be overlaid on
 KEGG
 pathways. The problem is that the bacterium I work on is not
 a KEGG
 organism. I have a draft genome and I have used KASS to find
 KEGG
 Orthology assignments for each of the genes. Is it possible,
 somehow,
 to still use Pathview? For example, instead of calling the
 pathview
 function with species = "hsa", would it be possible to
 provide a
 custom set of KO assignments?

[[elided Yahoo spam]]

 Cheers,
 Iain