Hi Dermot,
John Zhang <jzhang at="" jimmy.harvard.edu=""> writes:
>
>>
>>I've been trying to use AnnBuilder (also Resourcerer|) to build
>>annotation package for Bos Taurus and I know I need to edit
"species"
>>in a number of functions (I expect) in order to do this. I have been
>>following discussion (links below) on this topic which indicate that
I
>>need to edit the "getSrcUrl" function in AnnBuilder. However, I
can't
>>find this function or "downloadSourceData.R " anywhere. Where is
this
>>function and how can I edit it ? Thanks in advance.
>>
>
> getSrcUrl is in the file named getSrcUrl.R. It will be hard to get
it to work by
> editing functions within R as some of the functions are not included
in the
> NAMESPACE. You will have to get the source code and work from there.
There are
> several places you will need to change (basically by adding code to
handle a new
> organism)
To get the source code, you can either:
1. Install Subversion (http://subversion.tigris.org/), get a working
copy of the devel sources for AnnBuilder:
svn co --username=readonly --password=readonly
https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/AnnBuilder
or
2. Download the source package (.tar.gz) from here:
http://bioconductor.org/packages/release/bioc/html/AnnBuilder.html
Learning svn may seem intimidating, but you can get started in small
steps. Installing and doing a checkout to download a copy of the
source code is a good way to start.
+ seth
--
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research
Center
http://bioconductor.org
>
>I've been trying to use AnnBuilder (also Resourcerer|) to build
>annotation package for Bos Taurus and I know I need to edit
"species"
>in a number of functions (I expect) in order to do this. I have been
>following discussion (links below) on this topic which indicate that
I
>need to edit the "getSrcUrl" function in AnnBuilder. However, I can't
>find this function or "downloadSourceData.R " anywhere. Where is this
>function and how can I edit it ? Thanks in advance.
>
getSrcUrl is in the file named getSrcUrl.R. It will be hard to get it
to work by
editing functions within R as some of the functions are not included
in the
NAMESPACE. You will have to get the source code and work from there.
There are
several places you will need to change (basically by adding code to
handle a new
organism)
>
>
>https://stat.ethz.ch/pipermail/bioconductor/2007-February/016192.html
>
>
>
>https://stat.ethz.ch/pipermail/bioconductor/2006-August/014074.html
>
>
>
>https://stat.ethz.ch/pipermail/bioconductor/2007-February/016200.html
>
>
>
>Dermot
>
>
> [[alternative HTML version deleted]]
>
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Jianhua Zhang
Department of Medical Oncology
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084
Hi, Dermot,
Bos Taurus is a fairly popular organism. I will try to make AnnBuilder
support
Bos Taurus. It might take a couple of days. But I have to commit the
modification to bioc 2.1 because BioC 2.0 has just been released.
best
nianhua
Hi, Dermot,
I have updated AnnBuilder to support cattle. Please use "Bos taurus"
as organism name when you invoke ABPkgBuilder. Here is an example
script:
library(AnnBuilder)
ABPkgBuilder(baseName="bovine.GenBankID",
baseMapType="gbNRef",
pkgName="bovine",
pkgPath=".",
organism="Bos taurus",
otherSrc="bovine.EntrezGeneID",
version="1.1.0",
author=list(
authors="myname",
maintainer="myname <user at="" email.com="">"
)
)
"bovine.GenBankID" and "bovine.EntrezGeneID" are the mapping I
extracted from Affymetrix's annotation file for gene chip Bovine. I
also want to list the QC data here just to give a sense of annotation
coverage:
Mappings found for probe based rda files:
bovineACCNUM found 24117 of 24128
bovineCHRLOC found 9267 of 24128
bovineCHR found 18687 of 24128
bovineENTREZID found 19415 of 24128
bovineENZYME found 1017 of 24128
bovineGENENAME found 19045 of 24128
bovineGO found 10914 of 24128
bovineMAP found 245 of 24128
bovinePATH found 2131 of 24128
bovinePMID found 5747 of 24128
bovineREFSEQ found 18740 of 24128
bovineSUMFUNC found 0 of 24128
bovineSYMBOL found 19045 of 24128
bovineUNIGENE found 18952 of 24128
Mappings found for non-probe based rda files:
bovineENZYME2PROBE found 358
bovineGO2ALLPROBES found 5178
bovineGO2PROBE found 3218
bovineORGANISM found 1
bovinePATH2PROBE found 165
bovinePFAM found 14273
bovinePMID2PROBE found 2929
bovinePROSITE found 9818
In regarding to your question about Resourcerer, I am sure Jianhua,
the author of the Resourcerer package, will be the most helpful
resource. Speaking with my limited knowledge of Resourcerer, I think
no modification is required for function "getResourcerer" and you want
to specify organism name as "cattle". The function "resourcerer2BioC"
may not support cattle out of the box. One possible solution is to add
a mapping between "cattle" and "Bos taurus" inside the function code.
But there must be other better solutions as well.
cheers
nianhua
Dermot Morris wrote:
> Hi Nianhua,
>
> That would be a very useful development. Does Resourcerer also have
> some
> Additional functions that need to be changed to accommodate "Bos
Taurus"
> or is it dependent on calls to the same function as AnnBuilder? It's
> been a few weeks since I last looked.
>
> There is no rush - any time in the next couple of weeks will be fine
by
> me!
>
> Dermot
