Question: AnnBuilder problem
0
gravatar for Yihuan Xu
11.8 years ago by
Yihuan Xu130
Yihuan Xu130 wrote:
Dear all, I used AnnBuilder to annotate a customized mouse arrays. A folder 'costommice' is generated. However I don't know how to use it. How can I install it in R? Can I use it as KEGG package? Thank you. Yihuan Here is the code I used: library(AnnBuilder) myBase <- "C:\\TJU\\Siracusa\\GSEA\\annotation" myBaseType <-'gb' mySrcUrls <- getSrcUrl("all", "Mus musculus") myDir <- "C:\\TJU\\Siracusa\\annbuilder" ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = myBaseType, pkgName = "custommice", pkgPath = myDir, organism = "Mus musculus", version = "1.1.0", author = list(authors = "Yihuan Xu", maintainer = "yihuan.xu at jefferson.edu"), fromWeb = TRUE)
organism annotate annbuilder • 532 views
ADD COMMENTlink modified 11.8 years ago by Martin Morgan ♦♦ 23k • written 11.8 years ago by Yihuan Xu130
Answer: AnnBuilder problem
0
gravatar for Marc Carlson
11.8 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Yihuan Xu wrote: > Dear all, > > I used AnnBuilder to annotate a customized mouse arrays. A folder > 'costommice' is generated. However I don't know how to use it. How can I > install it in R? Can I use it as KEGG package? > > Thank you. > > Yihuan > > Here is the code I used: > > library(AnnBuilder) > myBase <- "C:\\TJU\\Siracusa\\GSEA\\annotation" > myBaseType <-'gb' > mySrcUrls <- getSrcUrl("all", "Mus musculus") > myDir <- "C:\\TJU\\Siracusa\\annbuilder" > ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = > myBaseType, pkgName = "custommice", > pkgPath = myDir, organism = "Mus musculus", version = "1.1.0", > author = list(authors = "Yihuan Xu", maintainer = > "yihuan.xu at jefferson.edu"), fromWeb = TRUE) > > _______________________________________________ > 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 > > If you have access to a unix machine you want to go to the dir where your newly minted customice dir is at and type something like this: R CMD INSTALL custommice Then launch R and say: library("custommice") However it looks like you are using windows, so you might want to go check out the much more complex instructions at the following site: http://www.murdoch-sutherland.com/Rtools/ I hope this helps, Marc
ADD COMMENTlink written 11.8 years ago by Marc Carlson7.2k
Answer: AnnBuilder problem
0
gravatar for Martin Morgan
11.8 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:
Marc Carlson <mcarlson at="" fhcrc.org=""> writes: > Yihuan Xu wrote: >> Dear all, >> >> I used AnnBuilder to annotate a customized mouse arrays. A folder >> 'costommice' is generated. However I don't know how to use it. How can I >> install it in R? Can I use it as KEGG package? >> >> Thank you. >> >> Yihuan >> >> Here is the code I used: >> >> library(AnnBuilder) >> myBase <- "C:\\TJU\\Siracusa\\GSEA\\annotation" >> myBaseType <-'gb' >> mySrcUrls <- getSrcUrl("all", "Mus musculus") >> myDir <- "C:\\TJU\\Siracusa\\annbuilder" >> ABPkgBuilder(baseName = myBase, srcUrls = mySrcUrls, baseMapType = >> myBaseType, pkgName = "custommice", >> pkgPath = myDir, organism = "Mus musculus", version = "1.1.0", >> author = list(authors = "Yihuan Xu", maintainer = >> "yihuan.xu at jefferson.edu"), fromWeb = TRUE) >> >> _______________________________________________ >> 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 >> >> > If you have access to a unix machine you want to go to the dir where > your newly minted customice dir is at and type something like this: > > R CMD INSTALL custommice > > > Then launch R and say: > > library("custommice") > > > However it looks like you are using windows, so you might want to go > check out the much more complex instructions at the following site: > > http://www.murdoch-sutherland.com/Rtools/ Actually, the windows instructions are getting easier. There's an 'Rtools installer' here http://www.murdoch-sutherland.com/Rtools/installer.html Apparently, this provides everything required to build and install packages (but not documentation) on Windows. Install R. Then run the installer, choosing 'Package authoring installation' when asked to select components, and then c:\MyDir> R CMD INSTALL --docs=none custommice I have not set up a system 'naive' enough to know that this works completely smoothly, and would love to hear any feedback. Martin > I hope this helps, > > > Marc > > _______________________________________________ > 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 -- Martin Morgan Bioconductor / Computational Biology http://bioconductor.org
ADD COMMENTlink written 11.8 years ago by Martin Morgan ♦♦ 23k
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