Re: [R] Nodes & edges with similarity matrix

z which contains the code to plot graph objects from the graph package. Without further details, for example the output of sessionInfo(), it is difficult to say. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userp

Re: [R] Nodes & edges with similarity matrix

Along with the example I gave using graphAM, you might also want to look at the help page for the distGraph class which may be more directly what you want: library("graph") class ? distGraph __ R-help@stat.math.ethz.ch mailing list https://stat.ethz

Re: [R] Nodes & edges with similarity matrix

mode="directed") To visualize your graph you can use the Rgraphviz package which will allow you to do: plot(g) You might also be interested in the RBGL package which provides many powerful graph algorithms. All of these packages are available via Bioconductor (no bio required)

Re: [R] Suspected memory leak with R v.2.5.x and large matrices with dimnames set

you from getting things done, or just a concern that there is a leak that needs fixing? It is worth noting that the internal handling of character vectors has changed in R-devel and so IMO testing there would make sense before persuing this further, I suspect your results will be di

Re: [R] A clean way to initialize class slot of type "numeric" vector

do this? This is quite a common situation but I can't > seem to find a way out. Any help would be really appreciated. Thank > you. How about: setClass("foo", representation(members="numeric"), prototype(members=numeric(0))) That is, use a zero-le

Re: [R] Need Help: Installing/Using xtable package

ing the methods directory (tsk tsk). But the addition fixes breakage that was occuring due to internal xtable helper functions being masked. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/

Re: [R] tcltk error on Linux

t some needed improvements to the methods packages. These are being worked on. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/ __ R-help@stat.ma

Re: [R] S4 methods: unable to find an inherited method

"url" > Any help as to why I'm getting the inherited method error would be > great. You either need to add a method specialized on the url class (warning, url is not an S4 class, there will be tricks required). Or you need to pass in an xcms

Re: [R] Catch errors

tag <- tryCatch({ print("inside tryCatch") if (fail) stop("forcing an error") 0 }, error=function(e) { print("caught an error") 1 }) tag + seth -- Seth Falcon | Computationa

Re: [R] Problems with expresso

making sure all of your packages are up to date: ## *new* R session, no saved data loaded source("http://bioconductor.org/biocLite.R";) biocLite("Biobase") library("Biobase") update.packges(repos=biocReposList()) + seth -- Seth Falcon | Computational Biolo

Re: [R] initalizing and checking validity of S4 classes

7; might initialize the inherited slots of the object, > but the object itself is of the derived class and could well be > invalid 'invalid' after the base class has finished with initialize). This is a good point. It suggests that, at least, one must initialize all non-inher

Re: [R] R and HTTP get 'has file changed'

pposed to looping the above: h <- multiTextGatherer(urls) junk <- getURIAsynchronous(urls, write=h, header=TRUE, nobody=TRUE) yourInfo <- sapply(h, function(x) something(x$value())) I've used this in the pkgDepTools package to

Re: [R] installing Rgraphviz under fedora 5

will have problems with graphviz 2.13 and that you will need to use graphviz 2.12. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz

Re: [R] locked environment and inheritance

class and lock it back or > something? I think that might be possible, but that doesn't make it a good idea :-) > Please let me know if that makes sense ? > I appreciate your comments. It might help to understand what your are trying to achieve overall. Perhaps there are other appro

Re: [R] locked environment and inheritance

quot;myPkg" environment (and not global environment). > > Using: > > > setClass("myS4class", representation("otherS4class", mydata = > "numeric"), where = topenv()) have you tried just omitting the where argument? Classes will get

Re: [R] Affycoretools

ibxml2? + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-proj

Re: [R] summing up colum values for unique IDs when multiple ID's exist in data frame

Nms <- names(df)[-whID] ans <- lapply(colNms, function(cn) { unlist(lapply(idIdx, function(x) sum(df[[cn]][x])), use.names=FALSE) }) attributes(ans) <- list(names=colNms, row.names=names(idIdx),

Re: [R] S4 object slot of type 'call'

of this is that you can write a few methods for NullCall and in many cases avoid explicit tests like: if (class(obj) == "NullCall") ... else ... For example, you could define a show metho that printed 'NULL' or something. It is also possible to define a class union and u

Re: [R] accessing unexported functions

ike pkgEnv = getNamespace("MyPackage") attach(pkgEnv) You might also be interested in assignInNamespace -- perhaps you can add you function to the package's name space and then call it using :::. Be warned, this is the wrong way to solve a long-term problem. Bad things will happen

Re: [R] questions on package of KEGG

n't know how to do it in the same way for > KEGG in R? Many Thanks!! Hua I think you should ask this question on the bioconductor list. http://www.bioconductor.org/docs/postingGuide.html + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Res

Re: [R] function name collision

h package, you should get its version of union. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEAS

Re: [R] names of objects in .rda

ge objects or large collections of objects. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the

Re: [R] Unit Testing Frameworks: summary and brief discussion

ror/warning message. I'm not sure how much benefit there is to that since it basically means putting the error message in two places, but I suppose it can be useful to make sure that any formatting of inputs is being done properly. + seth -- Seth Falcon | Computational Biology | F

Re: [R] unable to find inherited method for function "edges", for signature "ugsh", "missing"

")) >> edges(ug) > Error in function (classes, fdef, mtable) : > unable to find an inherited method for function "edges", for > signature "ugsh", "missing" > Execution halted > > (I never use the function nodeJoint in my .Rd fil

Re: [R] apply problem

e a data.frame is a list. But the return value will be a list, not a data.frame. I think for loops get a bad wrap. There are times when they are appropriate and even optimal in R programming. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center

Re: [R] Subsetting list of vectors with list of (boolean) vectors?

lt <- [magic box involving subset) result <- aPGI[aPGItest[[1]]] >> result > [[1]] > [1] "864" > + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ [EMAIL P

Re: [R] Method dispatch for print() in package its

ric for S4 classes and leave print alone. Not sure if that helps you. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ [EMAIL PROTECTED] mailing list https://stat.ethz.ch/mailman/listin

Re: [R] how to reverse a list

ist(inList) split(nms, vals) } + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/lis

Re: [R] RMySQL *was* working...

data frame, and so forth. > > Today, dbDriver() threw an error: > >> dbDriver(MySQL) Error in function (classes, fdef, mtable) : unable > to find an inherited method for function "dbDriver", for signature > "function" Do you mean dbDriver("MySQL")

Re: [R] Over-writing functions from other packages? What is a good strategy??

Depend on it. This would avoid graph::edges polluting the search path when Rgraphviz gets loaded. This is a reason that import might be preferred over Depends for packages that have namespaces. Finally, if you were depending on graph and not Rgraphviz, then you could rename graph::edges when you impo

Re: [R] getting ess/emacs to link with a remote instance of R

running remotely. * I have never had success getting help to work via ESS when running R remotely. YMMV. * You may find that sending commands to the remote session without echoing is much faster. So you might try C-u C-c C-r to send a region. + seth -- Seth Falcon | Computati

Re: [R] Fast lookup in ragged array

ay hashed environments work is that a vector is initialized to the desired size and collisions are resolved using chaining. To reduce collisions and have a more efficient hashtable, you want to have more slots in the vector than items since the hash function is rarely perfect for your data. + seth

Re: [R] Fast lookup in ragged array

erestimating means that the underlying hashtable will need to be resized and this has a performance impact. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.eth

Re: [R] Fast lookup in ragged array

searchedBranched = new.env(hash=TRUE, parent=emptyenv(), size=X) where X is an estimate of the number of branches you will search. Using an environment implies you will need unique character names for each subgraph. Do you have that? If not, you could concatenate node names. For a 200 node graph,

Re: [R] Sweave question: prevent expansion of unevaluated reused code chunk

"Kevin R. Coombes" <[EMAIL PROTECTED]> writes: > [2] You are also correct that there is no advantage if I just call > them "chunk1" and "chunk2". But if I call them something more > interesting, like "perform.quantile.normalization" or > "truncate.and.log.transform", > then I can use this structure

Re: [R] Sweave question: prevent expansion of unevaluated reused code chunk

arkers are an internal detail of the document and so must of the time these never appear in the rendered output. Even in your example, won't it be confusing that <> and <> won't have appeared in labels earlier in the rendered document? + seth -- Seth Falcon | Computational B

Re: [R] RMySQL on win32

> should just install RSQLite from CRAN? Well, if you don't need MySQL, then SQLite and RSQLite will get you going. If you do need MySQL, you can try RODBC. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org

Re: [R] Download packages problem.

t is rather difficult to imagine that you will get any useful help. Please have a look at the posting guide and send an update. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help

Re: [R] Error loading a dependency in a package: missing namespace?

es, you cannot do import(pkg) in the NAMESPACE file if pkg doesn't itself have a NAMESPACE file. So try just removing that from your NAMESPACE file. + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __

Re: [R] from function to its name?

"Ido M. Tamir" <[EMAIL PROTECTED]> writes: > I wanted to pass a vector of functions as an argument to a function to do > some > calculations and put the results in a list where each list entry has > the "name" of the function. > I thought I could either pass a vector of function names as charact

Re: [R] object is not subsettable

r. The code example is just trying to count the number of GO Terms that have "chromosome" in their description. You can achieve this as follows: hasChr <- eapply(GOTERM, function(x) length(grep("chromosome", Term(x sum(unlist(hasChr)) + seth -- Seth Falcon | Co

Re: [R] help with RMySQL

"Ravi S. Shankar" <[EMAIL PROTECTED]> writes: > Hi R users, > > I am using RMySQL to connect to a database in MySQL. > > I have 3 questions. > > > > 1)When I give the following command > > dbListTables(con) > > > > I get the output > > > > stack imbalance in .Call, 142 then 143 > > stack im

Re: [R] Problems with 'delay'/'delayedAssign' when installing data package

Hi Wolfram, Wolfram Fischer <[EMAIL PROTECTED]> writes: > I downloaded: > http://www.bioconductor.org/data/metaData/hgu95av2_1.7.0.tar.gz > described as: > Package: hgu95av2 > Title: A data package containing annotation data for hgu95av2 > Version: 1.7.0 > Created: Wed Jan

Re: [R] RES: RdbiPgSQL in R 2.4.1

"Eduardo Dutra de Armas" <[EMAIL PROTECTED]> writes: > Hi Seth > I'm running R on WinXP. On the first time I've installed Rdbi and RdbiPgSQL > from zip files not downloaded from Bioconductor. No problems during > installation. > Now I tried to install from biocLite and a message was showed for Rdb

Re: [R] RdbiPgSQL in R 2.4.1

Hi Eduardo, It would probably be best to send question regarding Bioconductor packages to the bioconductor email list. "Eduardo Dutra de Armas" <[EMAIL PROTECTED]> writes: > Hi R-users > > I recently downloaded RdbiPgSQL 1.8.0 and Rdbi 1.8.0 from Bioconductor to be > installed under R 2.4.1. > >

Re: [R] R for bioinformatics

Benoit Ballester <[EMAIL PROTECTED]> writes: > Hi, > > I was wondering if someone could tell me more about this book, (if it's > a good or bad one). > I can't find it, as it seems that O'Reilly doesn't publish any more. I've never seen a copy so I can't comment about its quality (has anyone seen

Re: [R] help with regexpr in gsub

"Kimpel, Mark William" <[EMAIL PROTECTED]> writes: > I have a very long vector of character strings of the format > "GO:0008104.ISS" and need to strip off the dot and anything that follows > it. There are always 10 characters before the dot. The actual characters > and the number of them after the

Re: [R] listing all functions in R

"Earl F. Glynn" <[EMAIL PROTECTED]> writes: > "Prof Brian Ripley" <[EMAIL PROTECTED]> wrote in message > news:[EMAIL PROTECTED] >> Here is a reasonable shot: >> >> findfuns <- function(x) { >> if(require(x, character.only=TRUE)) { >>env <- paste("package", x, sep=":") >>nm <- l

Re: [R] RSQLite NA on input

Hi Richard, It would help if you provided a bit more on how you are going about the import (along with your version of R and RSQLite). R Gott <[EMAIL PROTECTED]> writes: > I haev some .csv data files with missing values - eg below > > 1,'F','C04','X100',20.93,'C','B',7,8,7.5,2421,2230,2230,2,1,85

[R] [R-pkgs] RSQLite 0.4-18 sent to CRAN

files. This resolves performance issues and line ending quandries on Windows. * Fix for a bug in dbWriteTable when used to import text files; files lacking a trailing end of line marker can now be used. Questions? Send them to the r-sig-db mailing list. Best Wishes, + seth -- Seth

Re: [R] SQLite: When reading a table, a "\r" is padded onto the last column. Why?

Prof Brian Ripley <[EMAIL PROTECTED]> writes: > [I am not sure who is actually maintaining RSQLite, so am Cc: both the > stated maintainer and the person who prepared the package for > distribution. The posting guide asked you to contact the maintainer: > what response did _you_ get?] For the reco

Re: [R] package dependency tree

demonstrates the pkgDepTools package: [144] Seth Falcon. Modeling package dependencies using graphs. R News, 6(5):8-12, December 2006. + seth __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read t

Re: [R] biocondutor installation problem

I'm pretty sure your subject should be: Help configure R to use web proxy on RHEL4. You don't have a Bioconductor specific problem (yet). "Kesavan Asaithambi" <[EMAIL PROTECTED]> writes: >> source("http://www.bioconductor.org/biocLite.R";) > > Error in file(file, "r", encoding = encoding) : >

[R] BioC Advanced Course Jan 10th-12th (Space Still Available)

Hello all, There is still space available for the upcoming BioC Advanced Course being held in Seattle January 10th-12th. For details and registration, please visit: https://secure.bioconductor.org/biocadv/ Best Wishes, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer

Re: [R] RSQLite +textConnection()

"Alexander Nervedi" <[EMAIL PROTECTED]> writes: > Hi Seth, > > Thank you for taking the trouble to look. I have created some code > that simulates the problem. SOme additional observations are: > > a) After giving the error "Error in textConnection(readLines(f, n = > 2)) : all connections are in us

Re: [R] RSQLite +textConnection()

"Alexander Nervedi" <[EMAIL PROTECTED]> writes: > They are uptodate. When I run it on windows the i can load upto 200 > files, while on Linux it stops after loading 125. Could you provide as much of a reproducible example as possible (along with sessionInfo())? I will try and have a look. + set

Re: [R] RSQLite +textConnection()

"Alexander Nervedi" <[EMAIL PROTECTED]> writes: > Hi ! > > I am trying to read in 1000 really small text files. When on adams, R bails > out after reading 125 files with the error message > > Error in textConnection(readLines(f, n = 2)) : > all connections are in use Please try updating

Re: [R] RSQLite basic

Hi Alexander, "Alexander Nervedi" <[EMAIL PROTECTED]> writes: > However, this gives all kinds of errors when I run it on a linux box and I > am not sure what the error message is telling me. I thought I'd crave your > indulgence and ask for advice. > > >>m <- dbDriver("SQLite", max.con = 25) >>c

[R] ANN: BioC Advanced Course, Jan 10-12 in Seattle

://secure.bioconductor.org/biocadv/ + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] SNA packages/network package

> Bagatti Davide wrote: >> Hello everyone, >> >> I am an italian student who is working with packages SNA (social network >> analysis) and network. >> I ask you if there is a simple way to write a R-script using these packages >> to extract from an adjacency matrix the following things: >> >> -num

Re: [R] Rgraphviz -404 Page not found

"j.joshua thomas" <[EMAIL PROTECTED]> writes: > Again i have problem in locating the package for clique-graphs > I tried with BioConductor under Browse for packages, it doesn't work atall. > > Kindly guid me I think you already got an answer on the Bioconductor list: RBGL is likely the package yo

Re: [R] Forming SQL Query at run-time

"Rahul Thathoo" <[EMAIL PROTECTED]> writes: > Hi. > > I am trying to get data from mysql database using a couple of queries. > I do one query to find out the indexes. Then i need to use these > indexes in another query, but i keep getting errors. > > Here is something: > > numb <- dbSendQuery(con2

Re: [R] Install RMySQL with R 2.4.0

"Joe W. Byers" <[EMAIL PROTECTED]> writes: > Seth Falcon wrote: >> "Joe W. Byers" <[EMAIL PROTECTED]> writes: >> >>> I am having trouble as well with the new version of R 2.4. I downloaded >>> the gz file from the cran we

Re: [R] Install RMySQL with R 2.4.0

"Joe W. Byers" <[EMAIL PROTECTED]> writes: > I am having trouble as well with the new version of R 2.4. I downloaded > the gz file from the cran website, followed the instructions in the > README.win file and installed RMySQL. I have mysql installed under > c:\mysql not the program files dir

Re: [R] accesing MySQL through JDBC

"Your EPEC ICT Team - Ricardo Rodríguez" <[EMAIL PROTECTED]> writes: > Please, does R support JDBC access to MySQL databases? Could you point > me in the right direction to find some documents about this issue? Have you found the RMySQL package? It allows you to talk to MySQL databases from R. +

Re: [R] 'weaver' package problem

Hi Michael, Michael Kubovy <[EMAIL PROTECTED]> writes: > Hi Seth, > > The possibility of caching computations would be a great boon when > one is iteratively refining a paper; so I'm most grateful for your > work on this. Unfortunately I have a problem to report: > **testing Sweav

[R] [R-pkgs] DBI, RMySQL, RSQLite updated

(no feature changes). Best Wishes, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org ___ R-packages mailing list R-packages@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/r

Re: [R] Block comments in R?

Uwe Ligges <[EMAIL PROTECTED]> writes: > Use an editor that comments out a whole block which is what I do all the > time, e.g. use Tinn-R, Emacs or WinEdt, to mention just a few of > them. This, of course, works. The if(FALSE) approach does not because it requires the "comment" to be syntactical

Re: [R] New project: littler for GNU R

Jeffrey Horner <[EMAIL PROTECTED]> writes: > Seth Falcon wrote: >> Wow, looks neat. >> >> OS X users will be unhappy with your naming choice as the default >> filesystem there is not case-sensitive :-( >> >> IOW, r and R do the same thing. I woul

Re: [R] New project: littler for GNU R

Wow, looks neat. OS X users will be unhappy with your naming choice as the default filesystem there is not case-sensitive :-( IOW, r and R do the same thing. I would expect it to otherwise work on OS X so a change of some sort might be worthwhile. + seth ___

[R] ANN: R/BioC Intro Course Oct 9th-11th in Seattle

Hello all, We will be holding an R/BioC intro course in Seattle. The dates are October 9th-11th. For more information, please visit: https://secure.bioconductor.org/biocintro/ Best Wishes, + seth PS: At the moment we are using a self-signed SSL certificate (this is just as secur

Re: [R] Bioconductor installation errors

"Ge, Weigong*" <[EMAIL PROTECTED]> writes: > Hello, > > I follow the Bioconductor instruction (http://www.bioconductor.org/download > ) to install Biocoductor, there have > some errors: Please post questions about Bioconductor to the bioconductor mailing li

Re: [R] AffyChip Background Analysis

Gunther Höning <[EMAIL PROTECTED]> writes: > Dear list, > > I want to analyse some HG133Plus2.0 Affymetrix chips. > The first thing I intent to do, is just to perform a "background correction > (mas, rma, gcrma,...)" with the cel files. > Then I want to take a look at the files. > How can I do thi

Re: [R] Rgraphviz - neato layout - edge weights do not have an effect

Hi Franz, This might be better directed to the bioconductor mail list. Franz Quehenberger <[EMAIL PROTECTED]> writes: > Dear all, > > neato makes layouts according to a physical model in which the length > of the edges is determined by springs. The weight of the edge is the > strength of the spri

Re: [R] Rgraphviz installation Problem

"j.joshua thomas" <[EMAIL PROTECTED]> writes: > Dear Robert, > > Thanks for your time. > I have downloaded Rgraphviz (windows binary) from www.bioconductor.org > and put inside R2.3.0 library then i installed from the local zip > its says package 'graph' couldnot be loaded. > > Am i doing the ins

Re: [R] [R-pkgs] ANN: 'weaver' package, caching for Sweave

Hi again, Sorry for the noise, but I need to make a correction: Seth Falcon <[EMAIL PROTECTED]> writes: > To install: > > source("http://bioconductor.org/biocLite.R";) > biocLite("weaver") At present, the above install sequence will _only_ work if yo

[R] [R-pkgs] ANN: 'weaver' package, caching for Sweave

Hi all, I've added a new package 'weaver' to the BioC repository: http://www.bioconductor.org/packages/1.9/bioc/html/weaver.html The weaver package provides extensions to the Sweave utilities included in R's base package. The focus of the extensions is on caching computationally expensive (time

Re: [R] invisible() - does not return immediately as return() does

Matthias Burger <[EMAIL PROTECTED]> writes: > Hi, > > I stumbled across the following (unexpected for me) behavior after > replacing a return() statement in the middle of a function by invisible(). > > Example: > foo <- function() { cat("before\n"); return(); cat("after\n")} >>foo() > before > NUL

Re: [R] Running out of memory when using lapply

Hi Kamila, "Kamila Naxerova" <[EMAIL PROTECTED]> writes: > Hi all! > > I'm afraid I programmed something totally non-sensical and inefficient, > but I can't figure out how to do it better. > > I have a list of ~ 40 000 characters. I want to take each element at a > time, map it to a large data

Re: [R] RCurl

Rajarshi Guha <[EMAIL PROTECTED]> writes: > Hi, does anybody know where I might the RCurl package - the omegahat.org > server seems to be down The Bioconductor project hosts a mirror of a subset of Omegahat packages (RCurl is included). You can find the listing here: http://www.bioconductor.org

Re: [R] cluster analysis of microarray data

"Mahdi Osman" <[EMAIL PROTECTED]> writes: > Hi list, > > I am interested in cluster analysis of microarray data. The data was > generated using cDNA method and a loop design. > > > I was wondering if any one has a suggestion about which package I can > use to analyse such data. There are many pac

Re: [R] Drosophila Genome 2.0 annaffy annotation

Hi Marco, I'm pretty sure you want to resend your question to the Bioconductor mailing list. AFAICT your question is rather BioC specific and you will likely get a more helpful response there. + seth __ R-help@stat.math.ethz.ch mailing list https://st

Re: [R] Rgraphviz: Setting the edge width

Søren Højsgaard <[EMAIL PROTECTED]> writes: > I create an undirected graph with Rgraphviz (see code below). I would > like to make the edges thicker. Can anyone help on this?? Questions on Rgraphviz are best directed to the bioconductor mail list. I think you already discovered that, but for t

Re: [R] Installing bioconductor

Hi Kristine, "Kristine Kleivi" <[EMAIL PROTECTED]> writes: > I been trying to install bioconducter into R using the script on the > bioconductor home page. However, I get this error message: > > source("http://www.bioconductor.org/biocLite.R";) Error in file(file, > "r", encoding = encoding) : una

Re: [R] apologies if you aready received this ?

<[EMAIL PROTECTED]> writes: > Basically, I wrote a function called wait() > > > wait<-function() > { > cat("press return to continue") > unix("read stuff") > } Is readline what you want? See help(readline). __ R-help@stat.math.ethz.ch mailing list http

[R] BioC2006 Conference, Aug 3-4 in Seattle

Early registration ends July 1 BioC2006August 3-4 in Seattle, WA, USA http://bioconductor.org/BioC2006/ About BioC2006: This conference highlights developments within and beyond Bioconductor and provides a forum to discuss the use and design of software for analyzing data arising in biolog

Re: [R] Building packages in R - 'private' functions

"Antonio, Fabio Di Narzo" <[EMAIL PROTECTED]> writes: > 1. If you have time to change internal functions naming, you can rename > internal functions by putting a leading '.'. > Even without namespace, I have noticed there is no check for corresponding > docs for such functions. > > 2. If you don't

Re: [R] vague errors on R CMD check for very minimal S4-style package

"Roels, Steven" <[EMAIL PROTECTED]> writes: > Hello, > > I have a very minimal package "simplepkg" (DESCRIPTION, NAMESPACE, and > R) with S4 classes/methods (defines a class "foo" and a show method for > that class" - both the class and show method are exported). I can > seemingly install the pac

Re: [R] Install R problem

"Pramod Anugu" <[EMAIL PROTECTED]> writes: > I have copied R-2.3.0.tar.gx and uncompressed the directory R-2.3.0 is > created. > ./configure > Make > > Typed R in the directory /root/downloads/R-2.3.0/bin/exec > -bash-2.05b# pwd > /root/downloads/R-2.3.0/bin/exec > -bash-2.05b# R > Fatal error: R

Re: [R] Too many open files

"Omar Lakkis" <[EMAIL PROTECTED]> writes: > This may be more of an OS question ... > I have this call > > r = get.hist.quote(symbol, start= format(start, "%Y-%m-%d"), end= > format(end, "%Y-%m-%d")) > which does a url request > > in a loop and my program runs out of file handlers after few hundred

Re: [R] Manipulating code?

Johannes Hüsing <[EMAIL PROTECTED]> writes: > Dear expeRts, > I am currently struggling with the problem of finding > cut points for a set of stimulus variables. I would like > to obtain cut points iteratively for each variable by > re-applying a dichotomised variable in the model and then > recal

Re: [R] RMySQL on Mac OS 10.4

Ryan Hafen <[EMAIL PROTECTED]> writes: > > dbWriteTable(con, "test", rnorm(100)) > Error in .class1(object) : no direct or inherited method for function > 'dbWriteTable' for this call > > For more info, I am running OS X 10.4.6, R 2.2.1, I have compiled > RMySQL from source version 0.5-7, and

Re: [R] How to a handle an error in a loop

"Farrel Buchinsky" <[EMAIL PROTECTED]> writes: > No heaven on earth yet. > > how would I incorporate this kind of functionality into > Resultdt<-lapply(PGWide[,240:389], tdt) If you want to do more than one thing, you want to create an anonymous function. Here's an example: d <- runif(20, mi

Re: [R] accessing a SOAP based web service from R

Rajarshi Guha <[EMAIL PROTECTED]> writes: > Hi, > I have a number of web services that run on a server and can be > accessed via SOAP as well as by creating a specific URL. > > Now, for certain services, the argument that I need to send is about 10 > to 20 characters and the URL approach works f

Re: [R] programming advice?

"Charles Annis, P.E." <[EMAIL PROTECTED]> writes: > Dear R-helpers: > > I am doing some exploratory programming and am considering a routine that > has several other routines defined within it, so that I can avoid a large > and messy global re-programming to avoid naming conflicts. > > My questi

Re: [R] suppressing output

"Florian Koller" <[EMAIL PROTECTED]> writes: > Dear all, > > I am using the multinom() function from the nnet library within my own > code and I want to suppress multinom's output (#weights, iter 10, > 20...). > My code generates output too, and I don't want it to be mixed with the > output mes

Re: [R] load file RData which store in zip file

Prof Brian Ripley <[EMAIL PROTECTED]> writes: > [As an aside, I wonder whether compress=TRUE should not be the default for > binary save/save.image. It adds little time and may save a lot of disc > space.] Here's one user who thinks that is a great idea. I often have to remind developers who c

[R] Help understanding behavior of apply vs sapply

Hi, I was surprised that apply and sapply don't return the same results in the example below. Can someone tell me what I'm missing? > zls <- function(x) character(0) > m <- matrix(0, nrow=2, ncol=2) > apply(m, 1, zls) character(0) > sapply(m, zls) [[1]] character(0) [[2]] character(0) [[3]] c

Re: [R] setting argument defaults in setMethod

"Steven Lacey" <[EMAIL PROTECTED]> writes: > I want to set a default value in a method of a generic function. This seems > as though it should be possible. From R help on setMethod... > So, I try this... > > setGeneric("test",function(x,y){standardGeneric("test")}) > setMethod("test","numeric", >

Re: [R] installation problem with Biobase

Haleh, This question would be better asked on the Bioconductor mailing list. You haven't told us what version of R you are using. I suspect you have a version mismatch. With R 2.2.x you should be able to do the following to get MergeMaid installed: >From the R prompt do: source("http://biocond

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