Question: automatic data package maker
0
gravatar for Rafael A. Irizarry
14.9 years ago by
Rafael A. Irizarry2.3k wrote:
hi! is there a utility to automatically create a data package? if not, im making one cause i have tons of rdas lying around that i want to load using library instead of load. it will take as input the location of an rda, location to save the package, package title, package author, and text describing the data (for the Rd file) and create a package for that data set. any auxiliary untility that i should be using? -r
• 436 views
ADD COMMENTlink modified 14.9 years ago by Wolfgang Huber13k • written 14.9 years ago by Rafael A. Irizarry2.3k
Answer: automatic data package maker
0
gravatar for Tomas Radivoyevitch
14.9 years ago by
Tomas Radivoyevitch70 wrote:
Doing this manually has been taking me 1 to 2 hours a pop. Related to your question, a few weeks ago I tried to post the two questions below. Regarding the second of these and your question, perhaps the solution is to simply get everyone into the habit of making R data packages and sending them up to Bioconductor. It would be nice if manuscripts started coming with R scripts as "additional files" so that figures could be reproduced, and having the corresponding datasets up at bioconductor as R packages would certainly help. Q1: Does anyone have an automatic approach to grabbing GEO soft files and making esets out of them? Q2: Regarding R Data packages as an alternative to grabbing things from GEO, can anyone explain why there are so few (if any) GEO datasets also up at Bioconductor? I'm wondering if there's some sort of legal hindrance going on, or if it's just the leg work that's missing. ----- Original Message ----- From: "Rafael A. Irizarry" <ririzarr@jhsph.edu> To: <bioconductor@stat.math.ethz.ch> Sent: Friday, December 10, 2004 2:58 PM Subject: [BioC] automatic data package maker > hi! > > is there a utility to automatically create a data package? > > if not, im making one cause i have tons of rdas lying around that i want > to load using library instead of load. > > it will take as input the location of an rda, location to save the > package, package title, package author, and text describing the data > (for the Rd file) and create a package for that data set. > > any auxiliary untility that i should be using? > > -r > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
ADD COMMENTlink written 14.9 years ago by Tomas Radivoyevitch70
On Dec 10, 2004, at 1:36 PM, Tomas Radivoyevitch wrote: > Doing this manually has been taking me 1 to 2 hours a pop. > > Related to your question, a few weeks ago I tried to post the two > questions below. Regarding the second of these and your question, > perhaps the solution is to simply get everyone into the habit of > making R data packages and sending them up to Bioconductor. It would > be nice if manuscripts started coming with R scripts as "additional > files" so that figures could be reproduced, and having the > corresponding datasets up at bioconductor as R packages would > certainly help. > > Q1: Does anyone have an automatic approach to grabbing GEO soft > files and making esets out of them? I think not, but things like readGEOAnn could be used for such purposes. If they do not fit your requirements please let us know as we would happily take patches/improvements (on these and virtually any other functions). > > Q2: Regarding R Data packages as an alternative to grabbing things > from GEO, can anyone explain why there are so few (if any) GEO > datasets also up at Bioconductor? I'm wondering if there's some sort > of legal hindrance going on, or if it's just the leg work that's > missing. > Just time, if you have some please feel free, and let us know if there is anything we can do to help... Robert > > ----- Original Message ----- From: "Rafael A. Irizarry" > <ririzarr@jhsph.edu> > To: <bioconductor@stat.math.ethz.ch> > Sent: Friday, December 10, 2004 2:58 PM > Subject: [BioC] automatic data package maker > > >> hi! >> >> is there a utility to automatically create a data package? >> >> if not, im making one cause i have tons of rdas lying around that i >> want >> to load using library instead of load. >> >> it will take as input the location of an rda, location to save the >> package, package title, package author, and text describing the data >> (for the Rd file) and create a package for that data set. >> >> any auxiliary untility that i should be using? >> >> -r >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > +--------------------------------------------------------------------- -- ----+ | Robert Gentleman phone: (206) 667-7700 | | Head, Program in Computational Biology fax: | | Division of Public Health Sciences office: M2-B865 | | Fred Hutchinson Cancer Research Center email: rgentlem@fhcrc.org | +--------------------------------------------------------------------- -- ----+
ADD REPLYlink written 14.9 years ago by rgentleman5.5k
Answer: automatic data package maker
0
gravatar for Wolfgang Huber
14.9 years ago by
EMBL European Molecular Biology Laboratory
Wolfgang Huber13k wrote:
Rafael A. Irizarry wrote: >hi! > >is there a utility to automatically create a data package? > >if not, im making one cause i have tons of rdas lying around that i want >to load using library instead of load. > > Hi Rafa, have you looked at the function createPackage in Biobase ? I'd suggest to use it as a start and if necessary add functionality that you need. Best wishes Wolfgang
ADD COMMENTlink written 14.9 years ago by Wolfgang Huber13k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 300 users visited in the last hour