Thanks Martin for pointing this out. 

Does this mean other KEGG packages may not be up-to-date as well if they depend on KEGG.db? For example, I am interested in KEGGprofile package for enrichment analysis. Is KEGGprofile not up-to-date now?

Thanks

John




________________________________
 From: Martin Morgan <mtmorgan@fhcrc.org>
To: Dan Tenenbaum <dtenenba@fhcrc.org> 

onductor@r-project.org> 
Sent: Thursday, January 17, 2013 10:53 AM
Subject: Re: [BioC] error installing KEGGSOAP

On 1/17/2013 10:45 AM, Dan Tenenbaum wrote:

te:
>> Thanks Dan. For some other reason, I can't use devel version of R and/or
>> devel Bioconductor.... Is tere any other way of getting the list of genes
>> per KEGG pathway, and a list of available KEGG pathways?
>>
>
>
>  From a web browser you can do this to get the list of all pathways:
> http://rest.kegg.jp/list/pathway
> To restrict by organism, add the kegg organism code (in this case hsa
> for human):
> http://rest.kegg.jp/list/pathway/hsa
>
> To get the genes per kegg pathway:
> http://rest.kegg.jp/link/genes/path:hsa00010
>
> Or just show all info about the pathway:
> http://rest.kegg.jp/get/path:hsa00010
>
> ...and parse out the GENE section.
> For both of these last two URLs you need to do a bit of parsing.
> KEGGREST takes care of this for you.

Also, the KEGG.db package provides a now quite out-of-date version (because of 
changes in licensing requirements) of the KEGG data base.

> library(org.Hs.eg.db)
> # discover the columns that can be queried, and the format of the 'PATH' keys
> cols(org.Hs.eg.db)
  [1] "ENTREZID"     "PFAM"         "IPI"          "PROSITE"      "ACCNUM"
  [6] "ALIAS"        "CHR"          "CHRLOC"       "CHRLOCEND"    "ENZYME"
[11] "MAP"          "PATH"         "PMID"         "REFSEQ"       "SYMBOL"
[16] "UNIGENE"      "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS" "GENENAME"
[21] "UNIPROT"      "GO"           "EVIDENCE"     "ONTOLOGY"     "GOALL"
[26] "EVIDENCEALL"  "ONTOLOGYALL"  "OMIM"         "UCSCKG"
> head(keys(org.Hs.eg.db, "PATH"))
[1] "04610" "00232" "00983" "01100" "00380" "00970"
> head(select(org.Hs.eg.db, "00010", "ENTREZID", "PATH"))
    PATH ENTREZID
1 00010      124
2 00010      125
3 00010      126
4 00010      127
5 00010      128
6 00010      130
Warning message:
In .generateExtraRows(tab, keys, jointype) :
   'select' resulted in 1:many mapping between keys and return rows

Note that on loading KEGG.db we see this:

KEGG.db contains mappings based on older data because the original
   resource was removed from the the public domain before the most
   recent update was produced. This package should now be considered
   deprecated and future versions of Bioconductor may not have it
   available.  One possible alternative to consider is to look at the
   reactome.db package

>
> Dan
>
>
>
>
>> Many thanks for all your help,
>>
>> John
>>
>> ________________________________
>> From: Dan Tenenbaum <dtenenba@fhcrc.org>

>> Cc: Martin Morgan <mtmorgan@fhcrc.org>; "bioconductor@r-project.org"
>> <bioconductor@r-project.org>
>> Sent: Thursday, January 17, 2013 9:50 AM
>>
>> Subject: Re: [BioC] error installing KEGGSOAP
>>

te:
>>> Thanks Dan. what package is keggLink() from?
>>
>> It's from the KEGGREST package that Martin mentioned, which is only
>> available in the devel version of Bioconductor (the one that will be
>> installed if you use R-devel (aka R 3.0)).
>>
>> Dan
>>
>>
>>>
>>> John
>>>
>>> ________________________________
>>> From: Dan Tenenbaum <dtenenba@fhcrc.org>

>>> Cc: Martin Morgan <mtmorgan@fhcrc.org>; "bioconductor@r-project.org"
>>> <bioconductor@r-project.org>
>>> Sent: Thursday, January 17, 2013 7:39 AM
>>>
>>> Subject: Re: [BioC] error installing KEGGSOAP
>>>
>>> On Thu, Jan 17, 2013 at 7:14 AM, Dan Tenenbaum <dtenenba@fhcrc.org> wrote:

>>>> wrote:
>>>>> Thanks Martin. Is there a simple method to get a list of genes for a
>>>>> given pathway?
>>>>>
>>>>
>>>> This is how you would do it for human:
>>>> keggLink("hsa", "path:hsa00010")
>>>>
>>>
>>> Or more generally:
>>> keggLink("genes", "path:hsa00010")
>>>
>>> Dan
>>>
>>>
>>>> Dan
>>>>
>>>>
>>>>> John
>>>>>
>>>>>
>>>>> ________________________________
>>>>>   From: Martin Morgan <mtmorgan@fhcrc.org>
>>>>>
>>>>> Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>;
>>>>> "r-help@r-project.org" <r-help@r-project.org>
>>>>> Sent: Wednesday, January 16, 2013 10:38 PM
>>>>> Subject: Re: [BioC] error installing KEGGSOAP
>>>>>
>>>>> On 01/16/2013 05:58 PM, array chip wrote:
>>>>>> Hi, I am new to bioconductor, trying to install KEGGSOAP package, but
>>>>>> got warnings() when installing and error message when trying to load
>>>>>> the
>>>>>> package, can anyone suggest what went wrong?
>>>>>>
>>>>>> many thanks
>>>>>>
>>>>>> John
>>>>>>
>>>>>>
>>>>>>
>>>>>>> source("http://bioconductor.org/biocLite.R")
>>>>>> Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help
>>>>>>> biocLite("KEGGSOAP")
>>>>>> BioC_mirror: http://bioconductor.org
>>>>>> Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15.
>>>>>> Installing package(s) 'KEGGSOAP'
>>>>>> trying URL
>>>>>>
>>>>>> 'http://bioconductor.org/packages/2.11/bioc/bin/windows/contrib/2.15/KEGGSOAP_1.32.0.zip'
>>>>>> Content type 'application/zip' length 69037 bytes (67 Kb)
>>>>>> opened URL
>>>>>> downloaded 67 Kb
>>>>>>
>>>>>> package â€˜KEGGSOAPâ€™ successfully unpacked and MD5 sums checked
>>>>>>
>>>>>> The downloaded binary packages are in
>>>>>> Â Â Â Â Â Â Â
>>>>>> C:\Users\yzhang\AppData\Local\Temp\RtmpawAjwx\downloaded_packages
>>>>>> Warning message:
>>>>>> installed directory not writable, cannot update packages 'acepack',
>>>>>> 'actuar', 'ada', 'ade4', 'ade4TkGUI',
>>>>>> Â  'agricolae', 'akima', 'ape', 'aplpack', 'arules', 'bitops', 'boot',
>>>>>> 'Cairo', 'car', 'caTools', 'cba',
>>>>>> Â  'chron', 'class', 'clue', 'cluster', 'coda', 'colorspace',
>>>>>> 'CompQuadForm', 'corpcor', 'DAAG', 'date',
>>>>>> Â  'deldir', 'descr', 'deSolve', 'devtools', 'digest', 'diptest',
>>>>>> 'doBy', 'DoE.wrapper', 'e1071', 'effects',
>>>>>> Â  'ENmisc', 'epiR', 'eRm', 'evaluate', 'evd', 'FactoMineR', 'fArma',
>>>>>> 'fAssets', 'fBasics', 'fdrtool',
>>>>>> Â  'fExoticOptions', 'fExtremes', 'fGarch', 'fields', 'flexclust',
>>>>>> 'fMultivar', 'fNonlinear', 'fOptions',
>>>>>> Â  'forecast', 'foreign', 'fpc', 'fracdiff', 'fRegression', 'FrF2',
>>>>>> 'FrF2.catlg128', 'fTrading',
>>>>>> Â  'fUnitRoots', 'gamlss', 'gamlss.data', 'gamlss.dist', 'gclus',
>>>>>> 'gdata', 'geoR', 'GGally', 'ggm',
>>>>>> Â  'ggplot2', 'gmodels', 'gridBase', 'gWidgets', 'gWidgetstcltk', 'HH',
>>>>>> 'Hmisc', 'httr', 'igraph',
>>>>>> Â  'igraph0', 'inline', 'ipred', 'isa2', 'JavaGD', 'JGR', 'kernlab',
>>>>>> 'KernSmoot [... truncated]
>>>>>>
>>>>>>
>>>>>>> library(KEGGSOAP)
>>>>>> Loading required package: BiocGenerics
>>>>>>
>>>>>> Attaching package: â€˜BiocGenericsâ€™
>>>>>>
>>>>>> The following object(s) are masked from â€˜package:statsâ€™:
>>>>>>
>>>>>> Â Â Â  xtabs
>>>>>>
>>>>>> The following object(s) are masked from â€˜package:baseâ€™:
>>>>>>
>>>>>> Â Â Â  anyDuplicated, cbind, colnames, duplicated, eval, Filter, Find,
>>>>>> get, intersect, lapply, Map, mapply, mget, order, paste,
>>>>>> Â Â Â  pmax, pmax.int, pmin, pmin.int, Position, rbind, Reduce,
>>>>>> rep.int,
>>>>>> rownames, sapply, setdiff, table, tapply, union, unique
>>>>>>
>>>>>> failed to load HTTP resource
>>>>>> Error : .onLoad failed in loadNamespace() for 'KEGGSOAP', details:
>>>>>> Â  call: NULL
>>>>>> Â  error: 1: failed to load HTTP resource
>>>>>>
>>>>>> Error: package/namespace load failed for â€˜KEGGSOAPâ€™
>>>>>
>>>>> KEGG's SOAP service has been discontinued; the package has been replaced
>>>>> by
>>>>> KEGGREST, but KEGGREST is only available if using the 'devel' version of
>>>>> R, e.g.,
>>>>>
>>>>>    http://cran.fhcrc.org/bin/windows/base/rdevel.html
>>>>>
>>>>> Martin
>>>>>
>>>>>>
>>>>>>
>>>>>>> sessionInfo()
>>>>>> R version 2.15.1 (2012-06-22)
>>>>>> Platform: x86_64-pc-mingw32/x64 (64-bit)
>>>>>>
>>>>>> locale:
>>>>>> [1] LC_COLLATE=English_United States.1252Â  LC_CTYPE=English_United
>>>>>> States.1252Â Â
>>>>>> [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=CÂ Â Â Â Â Â Â Â
>>>>>> Â
>>>>>> Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â Â
>>>>>> [5] LC_TIME=English_United States.1252Â Â Â
>>>>>>
>>>>>> attached base packages:
>>>>>> [1] statsÂ Â Â Â  graphicsÂ  grDevices datasetsÂ  utilsÂ Â Â Â
>>>>>> methodsÂ
>>>>>> Â  baseÂ Â Â Â
>>>>>>
>>>>>> other attached packages:
>>>>>> [1] BiocGenerics_0.4.0Â  BiocInstaller_1.8.3
>>>>>>
>>>>>> loaded via a namespace (and not attached):
>>>>>> [1] codetools_0.2-8 RCurl_1.91-1.1Â  SSOAP_0.8-0Â Â Â Â  tools_2.15.1Â
>>>>>> Â
>>>>>> Â  XML_3.9-4.1Â Â Â Â  XMLSchema_0.7-2
>>>>>>     [[alternative HTML version deleted]]
>>>>>>
>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> Bioconductor mailing list
>>>>>> Bioconductor@r-project.org
>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>>> Search the archives:
>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Computational Biology / Fred Hutchinson Cancer Research Center
>>>>> 1100 Fairview Ave. N.
>>>>> PO Box 19024 Seattle, WA 98109
>>>>>
>>>>> Location: Arnold Building M1 B861
>>>>> Phone: (206) 667-2793
>>>>>         [[alternative HTML version deleted]]
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> Bioconductor mailing list
>>>>> Bioconductor@r-project.org
>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>>>> Search the archives:
>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>
>>


-- 
Dr. Martin Morgan, PhD
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109
	[[alternative HTML version deleted]]

