search for: systemsbiology

Hello, I am trying to write some code in R to communicate over sockets via the STOMP protocol (http://stomp.codehaus.org/Protocol). As you can see, a null byte (ASCII 0) is used as the "over" signal. I'd like to be able to do something like this: write.socket(socket, "CONNECT\nlogin: me\npasscode: pass\n\n\000") However, R does not like it when you put "\000"

Hi, When I use RSQLite's dbWriteTable(...) function, the columns in the db table frequently end up having "__1" (two underscores and a one) added to them. The names are unique within the table and contain no weird characters. For example a "position" column from a data.frame was written to the DB as "position__1". Does anyone understand how this name munging

Hi, I am trying to check a package via R CMD CHECK and it is failing with Error: '\s' is an unrecognized escape in character string starting "\s" The culprit looks something like this: gsub('\\s\\(.*\\)',"","this is a (test, man) dude") which is correctly escaped with the "\\"'s -- but it seems that R CMD CHECK is pre-escaping the

...> Roxane LEGAIE. > > > > > Roxane LEGAIE > Bioinformatician > -- > Warwick Systems Biology Centre > Coventry House > University of Warwick > Coventry CV4 7AL > U.K. > +44 (0)24 761 50332 > R.Legaie@warwick.ac.uk > http://www2.warwick.ac.uk/fac/sci/systemsbiology/ > > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem@fhcrc.org [[alternative HTML version deleted]]

I have successfully installed Rserv (http://stats.math.uni-augsburg.de/Rserve) on Mac OS, but I have trouble on two different linux platforms. R CMD INSTALL Rserve_0.3-10.tar.gz fails with this message ** libs gcc -g -O2 -I/usr/local/include -L/usr/local/lib Rserv.c -o Rserve \ -DDAEMON -O -I/usr/local/lib/R/include -Iinclude -I. -lR -L/usr/local/lib/R/bin -ldl -lcrypt

...odes (protein_summary_header, proteinprophet_details). <?xml version="1.0" encoding="UTF-8"?> <?xml-stylesheet type="text/xsl" href="http://localhost/ISB/data/interact-LFA1_C18_PME5R1.prot.xsl "?> <protein_summary xmlns="http://regis-web.systemsbiology.net/protXML" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v6.xsd " summary_xml="interact-LFA1_C18_PME5R1.prot.xml"> <protein_summary_header reference_database=&q...

I have a very large tab-delimited file, too big to store in memory via readLines() or read.delim(). Turns out I only need a few hundred of those lines to be read in. If it were not so large, I could read the entire file in and "grep" the lines I need. For such a large file; many calls to read.delim() with incrementing "skip" and "nrows" parameters, followed by grep()

In a quick search of the R website just now, I found no mention of a unit testing framework for R. I hope to find something in the style of Java's JUnit, or Python's unittest. Is such a thing available? Thanks, - Paul Shannon Institute for Systems Biology Seattle

Hi, I'm using gl1ce with family=binomial like so: >yy succ fail [1,] 76 23 [2,] 32 67 [3,] 56 43 ... [24,] 81 18 >xx c1219 c643 X1 0.04545455 0.64274145 X2 0.17723669 0.90392792 ... X24 0.80629054 0.12239320 >test.gl1ce <- gl1ce(yy ~ xx, family = binomial(link=logit), bound = 0.5 ) or >omit <- c(2,3) >test.gl1ce

...this website is still under development, just to show some possible cases, it will be re-built against R 2.15 and more case studies are coming. HTH Tengfei Another possibility for visual display of several kinds of data is RCytoscape, for which an example can be seen here: http://rcytoscape.systemsbiology.net/versions/current/gallery/TCGA/subnet.TCGA.02.0014.png This portrays 1) gene expression (green: under-expression; red: over-expression) 2) copy number (blue: high, black: low) 3) gene type (node shape: hexagons are kinases, arrows are ligands, diamonds are receptors, circles for ever...

...w >To: r-help at stat.math.ethz.ch >Message-ID: <411E9CBC.90207 at cs.ucr.edu> >Content-Type: text/plain; charset=us-ascii; format=flowed > > > >------------------------------ > >Message: 17 >Date: 14 Aug 2004 16:33:01 -0700 >From: Paul Shannon <pshannon at systemsbiology.org> >Subject: [R] Rserve needs (but cannot find) libR.a (or maybe it's .so) >To: R-help at stat.math.ethz.ch >Cc: simon.urbanek at math.uni-augsburg.de >Message-ID: <EXCHANGEfvuaQ20qXW2000013d7 at exchange.systemsbiology.net> > >I have successfully installed Rserv (h...

hello everyone, What is the method for selecting a coordinate from a graph with the mouse, if any such function exists? For example, we would like to select outliers in a scatter-plot with the mouse, or add figure legends with the mouse. There was a way to add figure legends with the mouse in Splus but I haven't found such functions in R. Thanks, Rich

Hi, Does anyone know the name of the package that includes a function for computing the lomb periodogram on irregular spaced ts data? I saw the package once ~ 1 month ago but cannot find it now ... , Rich

Hi, I am interested in a modification to LARS that allows for positive-only constraints in the variables (with details about how to implement this as described in section 3.4 of the Efron et al (2003) LARS paper). Before I dive into the "lars" package code myself, I was wondering if anyone knew of a version where this is available, or if another package that I have not found can do

Hi, I am making multiple calls to gzfile() via read.table(), e.g. > x <- read.table( gzfile( "xxx.gz" ) ) After i do this many times (I haven't counted, but probably between 50 and 100 times) I get the error message: Error in open.connection(file, "r") : unable to open connection In addition: Warning message: cannot open compressed file 'xxx.gz' however, I

Hi R gurus, I'm getting the following error when trying to build and install an R package: Error in untar2(tarfile, files, list, exdir) : unsupported entry type ?x? I build the package like so: R --no-init-file CMD build mypackage Then try to install it: sudo R --no-init-file CMD INSTALL mypackage.tar.gz ...which dies with the above error. I can extract the archive fine with tar -zxf, so

Hi, I'm trying to put together an R package. My library has dependencies on three other libraries: RSQLite, gaggle (a component of Bioconductor), and another package that is available as a download from the author's website. Is it possible to specify each of those dependencies in such a way that they will be automatically installed when a user installs my library? I'd like to save

I have a number simple R functions written for the biologists I work with. These functions will evolve, and the documentation will get steadily better. I hope to put them in a package on a local webserver, along with lots of help files, so that the users can easily update their installation. The functions are pure R, with no compiled code, but alias, I cannot figure out how to build this

Hi, After updating to R 2.7, my .Rprofile executes twice on startup. I confirmed this by putting in the following line: print("starting .Rprofile...") When I start R, I see: [1] "starting .Rprofile..." [1] "starting .Rprofile..." This seems like the obverse of the following FAQ:

I cannot modify the font size of the standard text items for the splineplot function found in the standard graphics package. Here is a tiny example, in which I try (but fail) to make the main title large. tbl = read.table ('http://www.ggobi.org/book/data/tips.csv', sep=',', header=T) spineplot (table (tbl$DAY, tbl$SEX), main='TIPS', cex.main=3) None of