Question: Getting annotation into GOstat
0
gravatar for Naomi Altman
6.8 years ago by
Naomi Altman6.0k
Naomi Altman6.0k wrote:
Hi, I have used GOstat with annotations already formated for Bioconductor. Now my colleague sent me a file with the annotations - e.g. Gene Name,GO ID,GO Description GRMZM5G802875,, GRMZM2G116557,6355,"regulation of transcription, DNA-dependent" GRMZM2G116557,5634,nucleus What functions do I need to use to get this information into a database so that I can run GOstat? Thanks, Naomi
transcription • 1.1k views
ADD COMMENTlink modified 18 months ago by j.baldauf0 • written 6.8 years ago by Naomi Altman6.0k
Answer: Getting annotation into GOstat
0
gravatar for James W. MacDonald
6.8 years ago by
United States
James W. MacDonald50k wrote:
Hi Naomi, On 10/29/2012 9:01 PM, Naomi Altman wrote: > Hi, > I have used GOstat with annotations already formated for > Bioconductor. Now my colleague sent me a file with the annotations - > e.g. > > Gene Name,GO ID,GO Description > > GRMZM5G802875,, > GRMZM2G116557,6355,"regulation of transcription, DNA-dependent" > GRMZM2G116557,5634,nucleus > > What functions do I need to use to get this information into a > database so that I can run GOstat? You don't say what species this is, and that turns out to be critical. Luckily my friend the googles says this is Zea mays, so I can give a partial answer. To do a hypergeometric test on these data you need at the very least an org.Zm.eg.db package, and unfortunately there isn't one. Luckily Marc Carlson is a stud, and you can now build one with about two lines of code: > library(AnnotationForge) > makeOrgPackageFromNCBI(version="1", author = "me <me at="" my.org="">", maintainer = "me <me at="" my.org="">", outputDir = ".", tax_id = "4577", genus = "Zea", species = "mays") wait for a while, and then do the usual installation steps (R CMD build, then check, then INSTALL). Then you can use the GOstats package, but since you don't have a chip-level .db package, you have to follow the instructions for using an org level package. I don't recall offhand how that goes, but IIRC you just have to specify the geneIDs and universeGeneIDs that pertain to your experiment (and these will be Entrez Gene IDs, so you have to use your new org.Zm.eg.db package to get them), as well as the org package. Best, Jim > > Thanks, > Naomi > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 6.8 years ago by James W. MacDonald50k
Answer: Getting annotation into GOstat
0
gravatar for j.baldauf
18 months ago by
j.baldauf0
j.baldauf0 wrote:

Hi Jim,

I guess there is still no org.Zm.eg.db package available (I couldn't find one), therefore, I tried to build it by my self, like you described it. But I failed building and installing the package, could you please give me some hints how to do that? I was trying to use Devtools, but got the following Error message: Could not find package root.

Here is my script, I am actually wasn't sure which arguments to use for build and install ()

biocLite("AnnotationForge")
library(AnnotationForge)
makeOrgPackageFromNCBI(version="1", author = "Jutta Baldauf", maintainer = "baldauf@uni-bonn.de", outputDir = ".", tax_id = "4577", genus = "Zea", species = "mays")

install.packages("devtools")
library(devtools)

#build the package
build()

# install the R package
install()

Thanks,

Jutta

 

ADD COMMENTlink written 18 months ago by j.baldauf0
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