similar to: DNAcopy package in R

Hello R Developers I am using DNACopy package http://bioconductor.org/packages/1.9/bioc/html/DNAcopy.html I am not able to figure out how to (if at all possible) to modify output format, namely, I am getting the following: "ID" "chrom" "loc.start" "loc.end" "num.mark" "seg.mean" Is it a way to get also median and standard deviation?

Dear all, Can anybody tell me how to export a 3d figure made with the plot3d function? I'm careless about whether it's still interactive or not in another format, as long I can get it out of R. Thanks! Alejandro Gonz?lez Departamento de Biodiversidad y Conservaci?n Real Jard?n Bot?nico Consejo Superior de Investigaciones Cient?ficas Claudio Moyano, 1 28014 Madrid, Spain Tel +0034

Hi All, I am using DNAcopy package in R for copy number analysis of 500K chip. The final output which I get from DNA copy is too big to be printed in a file. So I am getting an error as "reached getOption("max.print") -- omitted 475569 rows " Can somebody please provide me the pointers with how to increase the limit for max.print . Thanks, Pooja DISCLAIMER\

I apologize in advance for probably missing something obvious, but if someone could point me in the right direction I'd be grateful. This NOTE is not unique to our package (I list a few others, below). Package bcp has several Suggests (strucchange, for example). Then in an Rd file, we have if (require(strucchange)) { # Doing some examples making use of strucchange } The CRAN check

Full_Name: Adam B. Olshen Version: 1.3.1 OS: Linux Submission from: (NULL) (140.163.222.233) There appears to be a bug with write.table if the object being written is a matrix. Specifically, the option row.names=F gives an error. I have seen this problem repeated in the Windows implementation. An example is below. Adam Olshen olshena@mskcc.org This works: >

I am trying to build a package (GWASTools, submitted to Bioconductor) that uses the "sandwich" package. I have references to "sandwich" in DESCRIPTION: Imports: methods, DBI, RSQLite, sandwich, survival, DNAcopy and NAMESPACE: import(sandwich) In the code itself is a call to vcovHC: Vhat <- vcovHC(mod, type="HC0") I have sandwich version 2.2-7 installed.

Apologies for cross posting.... --------------------------------------------------------------------- CART Data Mining'04: First International CART(R) Conferences Focusing on the Data Mining technology of Leo Breiman, Jerome Friedman, Richard Olshen, Charles Stone (CART, MARS(R), TreeNet(tm), PRIM(tm)...) First Call For submissions

Dear R-experts, My problem is how to handle a 10GB data file containing genotype data. The file is in a particular format (Illumina final report) and needs to be altered and merged with phenotype data for further analysis. PERL seems to be an frequently used solution for this type of work, however I am inclined to think it should be doable with R. How do I open a text-file, line by line,

Instead of just upcasing them, can we add prefix ARCH_? --Venkatraman On Tue, Aug 25, 2009 at 2:36 AM, Eric Christopher<echristo at apple.com> wrote: > > On Aug 25, 2009, at 12:32 AM, Daniel Dunbar wrote: > >> Hi, >> >> I think I should rename the constants to be a little less likely to >> collide. I think just upcasing them might be good enough? > >

Hey So sorry to be a total newbie, but i'm just finding my feet with R. I heard on the grapevine i could recreate a scanned microarray image, or at least get a good graphic of it from a just a data file. I have .txt files for illumina beadarrays but no images cos the service we used didn't send them. The 'beadarray' package seems to require TIFFs to get the graphic output. Does

On Sun, Feb 2, 2014 at 11:50 AM, Anton Korobeynikov <anton at korobeynikov.info> wrote: > That's really cool! Should we add note to Release Notes? Definitely. I will add a note mentioning about this in ReleaseNotes.rst. > > On Sun, Feb 2, 2014 at 8:05 PM, Venkatraman Govindaraju > <venkatra at cs.wisc.edu> wrote: >> Thanks to Jakob's work on Sparcv9 ABI in

Hello everyone, I`m trying to normalize and analize an illumina SNP array. But when i`m trying to segmentate i`m getting an error: Error in sort(abs(diff(genomdat)))[1:n.keep] : only 0's may be mixed with negative subscripts. I`ve tried everything to fix this but the error still occours. Can anybody give me a tip? Thanks in advance! -- View this message in context:

I was under the impression that the tree method (e.g. as implemented in rpart) was insensitive to monotonic transformations of the dependent variable. e.g. Breiman Olshen et al. Classification and Regression Trees state "In a standard data structure [a tree] is invariant under all monotone transformations of individual ordered varaibles" (p. 57) However, I get very different results

Thanks to Jakob's work on Sparcv9 ABI in Clang and recent changes to Sparc code generator, I am happy to announce that Clang can self host itself on Linux/Sparc64 and on FreeBSD/Sparc64. However, it still fails on a few unit tests and nightly tests, primarily due to misaligned memory accesses in the code (See bugs 18482, 18500, 18502, 18536, 18693). Unlike other architectures, misaligned

On Wed, Oct 26, 2011 at 1:59 AM, Chris Lattner <clattner at apple.com> wrote: > > Fantastic.  A great place to start would be to investigate / screen various sparc related bugs in bugzilla to see if they are still relevant and present: > http://llvm.org/bugs/buglist.cgi?quicksearch=sparc > > This bug looks pretty fatal if it is actually real: >

I would prefer not to; they already live in a protected namespace, so there is no need to mangle them except to protect them from exuberant preprocessor defines, and this would be slightly out of style with other public uses of enumerations in LLVM. - Daniel On Tue, Aug 25, 2009 at 7:49 AM, Venkatraman Govindaraju<venkatra at cs.wisc.edu> wrote: > Instead of just upcasing them, can we

--- included message ---- Thus, my question is: *What common measures exists for ranking/measuring variable importance of participating variables in a CART model? And how can this be computed using R (for example, when using the rpart package)* ---end ---- Consider the following printout from rpart summary(rpart(time ~ age + ph.ecog + pat.karno, data=lung)) Node number 1: 228 observations,

Can I say that RPART is a modified algo of CART and PARTY a modified of CHAID? Thanks. ---- Chua Siang Li Consultant - Operations Research Acceval Pte Ltd Tel: 6297 8740 Email: siang.li.chua at acceval-intl.com Website: www.acceval-intl.com This message and any attachments (the "message"...{{dropped:12}}

Hello, The current version in SVN fails to compile in sparc machines since gcc defines "sparc" as a macro in sparc machines that expands to 1 (see below) but Triple.h defines "sparc" as a enum constant. $ cpp -dM /dev/null | grep sparc #define sparc 1 #define __sparc__ 1 #define __sparc 1 The attached patch fixes this problem by renaming sparc to sparc_. Thanks,

Hello, When I run LLC with option "-O0 -march=sparc" on following testcase, fast register allocator crashes with "UNREACHABLE executed" error. LLC generates code successfully with other standard register allocators available. $ cat call.ll define void @test() nounwind { entry: %0 = tail call i32 (...)* @foo() nounwind tail call void (...)* @bar() nounwind ret void }