Question: Editing AnnBuilder function "getSrcUrl"
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gravatar for Dermot Morris
12.6 years ago by
Dermot Morris40 wrote:
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ADD COMMENTlink modified 12.6 years ago by Nianhua Li870 • written 12.6 years ago by Dermot Morris40
Answer: Editing AnnBuilder function "getSrcUrl"
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gravatar for Seth Falcon
12.6 years ago by
Seth Falcon7.4k
Seth Falcon7.4k wrote:
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
ADD COMMENTlink written 12.6 years ago by Seth Falcon7.4k
Answer: Editing AnnBuilder function "getSrcUrl"
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gravatar for John Zhang
12.6 years ago by
John Zhang2.9k
John Zhang2.9k wrote:
> >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]] > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor Jianhua Zhang Department of Medical Oncology Dana-Farber Cancer Institute 44 Binney Street Boston, MA 02115-6084
ADD COMMENTlink written 12.6 years ago by John Zhang2.9k
Answer: Editing AnnBuilder function "getSrcUrl"
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gravatar for Nianhua Li
12.6 years ago by
Nianhua Li870
Nianhua Li870 wrote:
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
ADD COMMENTlink written 12.6 years ago by Nianhua Li870
Answer: Editing AnnBuilder function "getSrcUrl"
0
gravatar for Nianhua Li
12.6 years ago by
Nianhua Li870
Nianhua Li870 wrote:
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
ADD COMMENTlink written 12.6 years ago by Nianhua Li870
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