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Yue, Chen - BMD
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@yue-chen-bmd-3790
Last seen 9.6 years ago
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
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(Bucher Elmar)
----------------------------------------------------------------------
Message: 1
Date: Mon, 21 Dec 2009 11:53:56 +0200
From: Bucher Elmar <ext-elmar.bucher@vtt.fi>
Subject: [BioC] how to get gene list after hyperGTest (Yue, Chen -
BMD)
To: "bioconductor@stat.math.ethz.ch" <bioconductor@stat.math.ethz.ch>
Message-ID:
<94C37E6FD527C443B24CA58F2CCBC6C2C433D5D52E@VTTMAIL.ad.vtt.fi>
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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
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Today's Topics:
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----------------------------------------------------------------------
Message: 1
Date: Sat, 19 Dec 2009 12:36:26 -0600
From: "Yue, Chen - BMD" <yuechen@bsd.uchicago.edu>
Subject: [BioC] how to get gene list after hyperGTest
To: <bioconductor@stat.math.ethz.ch>
Message-ID:
<ad1fa15416eebc49a0fe4f8b0c8ad7c5158f35@adm- exchvs04.bsdad.uchicago.edu="">
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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
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