[BioC] Bioconductor Digest, Vol 82, Issue 20
xiangxue Guo
xiangxue_guo at yahoo.com
Mon Dec 21 20:06:09 CET 2009
Hi, Yue:
In case you have loaded libraries KEGG.db and KEGGgraph, you just add one more line:
ids <- as.character(ids)
it works for me very well
Xiang
--- On Mon, 12/21/09, Yue, Chen - BMD <yuechen at bsd.uchicago.edu> wrote:
> From: Yue, Chen - BMD <yuechen at bsd.uchicago.edu>
> Subject: Re: [BioC] Bioconductor Digest, Vol 82, Issue 20
> To: Ext-Elmar.Bucher at vtt.fi
> Cc: bioconductor at stat.math.ethz.ch
> Date: Monday, December 21, 2009, 10:11 AM
> Hi Bucher,
>
> Thanks for the information. I got an error after I tried to
> use KEGG.db. Here is what I did:
>
> >ids <- scan("D:/geneset.txt")
> > ids
> [1] 944750 944834 944794 944854 947139 947874 944866
> 945013 944925 945017 945081 945070
> >pathway <- mget(ids,KEGGEXTID2PATHID, ifnotfound =
> NA)
> Error in .checkKeysAreWellFormed(keys) :
> keys must be supplied in a character vector with no
> NAs
>
> Can you help? Thanks!
>
> Chen, Yue
>
>
> ________________________________
>
> From: bioconductor-bounces at stat.math.ethz.ch
> on behalf of bioconductor-request at stat.math.ethz.ch
> Sent: Mon 12/21/2009 5:00 AM
> To: bioconductor at stat.math.ethz.ch
> Subject: Bioconductor Digest, Vol 82, Issue 20
>
>
>
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> Today's Topics:
>
> 1. how to get gene list after hyperGTest
> (Yue, Chen - BMD)
> (Bucher Elmar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 21 Dec 2009 11:53:56 +0200
> From: Bucher Elmar <Ext-Elmar.Bucher at vtt.fi>
> Subject: [BioC] how to get gene list after hyperGTest (Yue,
> Chen -
> BMD)
> To: "bioconductor at stat.math.ethz.ch"
> <bioconductor at stat.math.ethz.ch>
> Message-ID:
> <94C37E6FD527C443B24CA58F2CCBC6C2C433D5D52E at VTTMAIL.ad.vtt.fi>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Chen Yue,
>
> To link genes to KEGG pathways try out this package:
> http://www.bioconductor.org/packages/2.5/data/annotation/html/KEGG.db.html
>
> KEGG.db is a AnnotationDbi package. Many kind of Metadata
> information is stored in such AnnotationDbi packages. So, if
> you understand to come along whit one AnnotationDbi you will
> be able to handle all the other AnnotationDbi. AnnotationDbi
> packages always end by ".db" in their name.
>
>
> To get you started:
>
> # install the package
> source("http://bioconductor.org/biocLite.R")
> biocLite("KEGG.db")
>
> # attach the package
> library(KEGG.db)
>
> # some man pages
> ?KEGG.db # basic man page
> ? ls("package:KEGG.db") # list all the object
> that exist in KEGG.db
> ?"KEGGEXTID2PATHID" # maybe the object you
> where looking for
>
> # some example
> ids <- c("7150","1281542","1274031")
> pathway = mget(ids, KEGGEXTID2PATHID, ifnotfound = NA)
> pathway
>
>
> Ps: This is what is written on the bioconductor homepages
> about AnnotationDbis ( http://www.bioconductor.org/overview ) :
> The Bioconductor project provides software for associating
> microarray and other g0enomic data in real time to
> biological metadata from web databases such as GenBank,
> LocusLink and PubMed (annotate package). Functions are also
> provided for incorporating the results of statistical
> analysis in HTML reports with links to annotation WWW
> resources.
> Software tools are available for assembling and processing
> genomic annotation data, from databases such as GenBank, the
> Gene Ontology Consortium, LocusLink, UniGene, the UCSC Human
> Genome Project (AnnotationDbi package).
> Data packages are distributed to provide mappings between
> different probe identifiers (e.g. Affy IDs, LocusLink,
> PubMed). Customized annotation libraries can also be
> assembled.
>
> Merry Christmas, Elmar
>
>
>
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch]
> On Behalf Of bioconductor-request at stat.math.ethz.ch
> Sent: 20 December 2009 13:00
> To: bioconductor at stat.math.ethz.ch
> Subject: Bioconductor Digest, Vol 82, Issue 19
>
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>
>
> Today's Topics:
>
> 1. how to get gene list after hyperGTest
> (Yue, Chen - BMD)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 19 Dec 2009 12:36:26 -0600
> From: "Yue, Chen - BMD" <yuechen at bsd.uchicago.edu>
> Subject: [BioC] how to get gene list after hyperGTest
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID:
> <AD1FA15416EEBC49A0FE4F8B0C8AD7C5158F35 at ADM-EXCHVS04.bsdad.uchicago.edu>
>
> Content-Type: text/plain
>
> Hi,
>
> I'm wondering if someone can help me with the result
> extraction after hyperGTest in GOstats package. After I
> obtained the hyperGTest result, I also want to know what
> category each input gene associates with, for example a KEGG
> pathway. What function should I use? Or should I use another
> package?
>
> Thanks!
>
> Chen, Yue
>
>
>
> This email is intended only for the use of the
> individua...{{dropped:20}}
>
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