search for: sdavis2

There are numerous tools like scons, make, ruffus, ant, rake, etc. that can be used to build complex pipelines based on task dependencies. These tools are written in a variety of languages, but I have not seen such a thing for R. Is anyone aware of a package available? The goal is to be able to develop robust bioinformatic pipelines driven by scripts written in R. Thanks, Sean

if I have.... QQQQ<-priceIts("QQQQ",quote="Close") QQQQ<-priceIts("QQQQ",quote="Close");plot(QQQQ) and then i want to do the same thing but say with IBM instead of QQQQ is there an easy way like replace qqqq/ibm Thanks in advance./Jonathan

I have a data set in which I have 5000 repeated measures on 6 subjects over time (varying intervals, but measurements for all individuals are at the same times). There are two states, a "resting" state (the majority of the time), and a perturbed state. I have a continuous measurement at each time point for each of the individuals. I would like to determine the "state"

I have a function that does some plotting. I then add lines to the plot. If executed one line at a time, there is not a problem. If I execute the function, though, I get: Error in ans[[1]] : subscript out of bounds This always occurs after the second lines command, and doesn't happen with all of my data points (some do not have errors). Any ideas? Thanks, Sean

...n Perl, to access other R and Bioconductor functions that I need such as t.test and ANOVA. This is very time-consuming, however. I am working in a Linux environment, and using R 2.1.0 Thanks for any help and suggestions! Mugdha Wagle ________________________________ From: Sean Davis [mailto:sdavis2 at mail.nih.gov] Sent: Fri 6/3/2005 8:03 AM To: Wagle, Mugdha Cc: r-help at stat.math.ethz.ch Subject: Re: [R] reading tables into R. . On Jun 3, 2005, at 8:40 AM, Wagle, Mugdha wrote: > I have been using R and Perl. When I read in a text file using the > read.table option, and I try to...

I have a binary vector and I want to find all "regions" of that vector that are runs of TRUE (or FALSE). > a <- rnorm(10) > b <- a<0.5 > b [1] TRUE TRUE TRUE FALSE TRUE FALSE TRUE TRUE TRUE TRUE My function would return something like a list: region[[1]] 1,3 region[[2]] 5,5 region[[3]] 7,10 Any ideas besides looping and setting start and ends directly?

Hi When I give the command: > heatmap.2(as.matrix(d),Rowv=as.dendrogram(hc.gene),Colv=FALSE,scale="row ",trace="none",col=greenred.colors(79)) The resulting heatmap has re-ordered my columns! This is time-course data, and I don't want my columns re-ordered! Note from the help: Rowv: determines if and how the _row_ dendrogram should be reordered.

> Dear expeRts, > > Currently, my colors are as follows: > mycol <- > c("blue1","blue2","blue3","blue4","black","yellow4","yellow3","yellow2","y > ellow1") > heatmap(snp, Rowv=NA, Colv=NA, col=mycol) > > However, I would like to have the following colors: > bright blue ->

Dear helpers Does R have a package that performs projection pursuit density estimation? Or anyone knows code in Matlab or C for example to do this? Thank you all Luis

I am working on a problem in which I have 2 groups of clusters, each of which was generated from the same original list of members. Within each group, the clusters cover the original list of members many times over. What I am interested in finding is the number of common elements in every pair of clusters when taking one from each group. In short, I need a FAST way of finding the number of

...FALSE. > > I'm attaching the latest version of the gregmisc package with > the corrected code. I've also added a couple of other > features while I was mucking about... > > > > -Greg > > > -----Original Message----- > > From: Sean Davis [mailto:sdavis2 at mail.nih.gov] > > Sent: Thursday, March 25, 2004 5:25 PM > > To: Warnes, Gregory R > > Subject: Quick "running" question > > > > > > Greg, > > > > I am starting to use running and do the following: > > > > > running(1:1...

Reposting to the group for input.... Thanks for any help you can provide. Sean ----- Original Message ----- From: <ale.ambrosi at unipd.it> To: <sdavis2 at mail.nih.gov> Sent: Monday, May 17, 2004 4:22 AM Subject: add objects to svm plot > > >at 06.38 14/05/2004 -0400, you wrote: > >It might be helpful if you could send your code to the list along with any > >error messages, etc. > > > >Sean > > Dear Sean...

I have a list of vectors $A "AB" "BC" "CD" $B "GF" "HG" "FH" "FJ" and I want to convert it into a dataframe of form A AB A BC A CD B GF B HG B FH B FJ Just can't quite come up with a nice "R" solution for it. Thanks, Sean

The entire message "[R] Several questions in R", originally sent to you by r-help-bounces at stat.math.ethz.ch (r-help-bounces at stat.math.ethz.ch), has been forwarded to you from the Antigen Quarantine area. This message may have been re-scanned by Antigen and handled according to the appropriate scan job's settings. <<Entire Message.eml>> -------------- next part

....math.ethz.ch] On Behalf Of I.Szentirmai Sent: Wednesday, February 22, 2006 7:04 AM To: r-help Subject: Re: [R] read.table missing values might be, but I have already found another solution: reat.table(file,sep="\t") Thanks, Istvan On Wed, 22 Feb 2006 07:54:49 -0500 Sean Davis <sdavis2 at mail.nih.gov> wrote: > Does using read.delim instead of read.table fix your >problem? > > Sean > > > On 2/22/06 7:40 AM, "I.Szentirmai" <I.Szentirmai at rug.nl> >wrote: > >> Dear R users, >> >> I'm trying to read data fro...

Can anyone share experience with opteron versus the xeon (woodcrest) for R under linux? I am looking at using 16-32Gb of ram in a workstation (as opposed to a server). Thanks in advance.... Sean

Thanks Sean! Your reply was very helpful. I already got almost what I wanted. I have some NA values but I will look if I can find them through bibliography or an external tool. Best Regards, Eleni On Mon, May 19, 2008 at 6:07 PM, Sean Davis <sdavis2@mail.nih.gov> wrote: > On Mon, May 19, 2008 at 10:47 AM, Eleni Christodoulou > <elenichri@gmail.com> wrote: > > Dear list, > > > > I am having a set of human oligo ids (H200006022 H200002025 H300004703 > > H200000442 H200005719 H300018350) which I want to map...

This is hopefully a simple question. I am trying to escape single quotes like so: abc's >> abc\'s However, I cannot find an easy way to do that with gsub: gsub("'","\\\\'","abc's") # returns "abc\\'s" How can I get a single \ in the output? Thanks, Sean

I have a table (output from table(factor1,factor2)). I would like to use write.table to output that table to a file. However, it seems that as.data.frame converts such a table to three columns, Var1, Var2, and Freq rather than converting to the data.frame with equivalent numbers of rows and columns. I can use write.matrix from the MASS package, but then I get no rownames. Any hints here?

Hello! I interest of using Perl for application of biostatistcs with R. I find your module on the cpan's site. But, I've a question: Could I use it with Mac OS X? Because I have this error: "Error: no suitable installation target found for package Statistics-R." If it's not possible with this script, how can I modify it ? Thanks a lot in advance!!! Beline