Re: [R] Trouble getting rms::survplot(..., n.risk=TRUE) to behave properly

the model. > > > -- > Frank E Harrell Jr Professor and Chairman School of Medicine > > Department of *Biostatistics* *Vanderbilt University* > > On Thu, Jun 2, 2016 at 10:55 AM, Steve Lianoglou <lianoglou.st...@gene.com> > wrote: > >> Hello foks, >

[R] Trouble getting rms::survplot(..., n.risk=TRUE) to behave properly

orm_1.0-5 [28] foreign_0.8-66 chron_2.3-47 zoo_1.7-13 === Thanks, -steve -- Steve Lianoglou Computational Biologist Genentech __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo

Re: [R] Scraping HTML using R

-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Computational Biologist Genentech

Re: [R] Fastest way to calculate quantile in large data.table

and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Computational Biologist Genentech

Re: [R] loops in R

list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Computational Biologist Genentech

Re: [R] NA's introduced by coercion

Hi Madhvi, First, please use reply-all when responding to emails form this list so that others can help (and benefit from) the discussion. Comment down below: On 26 Aug 2014, at 22:15, madhvi.gupta wrote: On 08/27/2014 10:42 AM, Steve Lianoglou wrote: Hi, On Tue, Aug 26, 2014 at 9:56 PM

Re: [R] NA's introduced by coercion

data after you convert it to a numeric -steve -- Steve Lianoglou Computational Biologist Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting

Re: [R] R, RStudio, and a server for my iPad.

=ioscommit=Search HTH, -steve -- Steve Lianoglou Computational Biologist Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide

Re: [R] R, RStudio, and a server for my iPad.

-605-7913 (Please call phone number above prior to faxing) Steve Lianoglou lianoglou.st...@gene.com 4/11/2014 5:23 PM Hi, On Fri, Apr 11, 2014 at 2:00 PM, John Sorkin jsor...@grecc.umaryland.edu wrote: I bemoan the fact that I can not run R or Rstudio on my iPad. I feel like

Re: [R] How to make a proper use of blocking in limma using voom

file, I think it would be easier for us if you copy/paste the output of `dput(targets)` and `dput(design)` after you create those object in a follow up email if it's necessary to write one. HTH, -steve -- Steve Lianoglou Computational Biologist Genentech

Re: [R] Trying to install package for LMER, getting a ton of errors

commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Computational Biologist Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting

Re: [R] a better method than a long expression with many OR clauses

]) == 3) 0) Unwind that one liner into it's individual parts to see who is doing what there. HTH, -steve -- Steve Lianoglou Computational Biologist Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] Thoughts for faster indexing

(whatever it might be). w * score }, by='id'] HTH, -steve -- Steve Lianoglou Computational Biologist Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org

Re: [R] Should there be an R-beginners list?

to host it, though. Given SO's critical mass, though, I think it's hard to argue against simply using that. -steve -- Steve Lianoglou Computational Biologist Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help

Re: [R] FW: Library update from version

provided several answers. This post in particular has a few answers from some people who know what they're doing w/ R, so probably a good place to start: http://stackoverflow.com/questions/1401904/painless-way-to-install-a-new-version-of-r-on-windows HTH, -steve -- Steve Lianoglou Computational

Re: [R] FW: Library update from version

Hi, On Mon, Sep 30, 2013 at 12:44 PM, Ista Zahn istaz...@gmail.com wrote: On Mon, Sep 30, 2013 at 2:49 PM, Steve Lianoglou lianoglou.st...@gene.com wrote: Hi, On Mon, Sep 30, 2013 at 11:12 AM, Cem Girit gi...@comcast.net wrote: Hello, I recently installed version 3.0.1

Re: [R] why is this a factor?

Hi, On Thu, Aug 29, 2013 at 3:03 PM, Rolf Turner rolf.tur...@xtra.co.nz wrote: On 29/08/13 12:10, Ista Zahn wrote: On Wed, Aug 28, 2013 at 7:44 PM, Steve Lianoglou lianoglou.st...@gene.com wrote: Hi, On Wed, Aug 28, 2013 at 3:58 PM, Ista Zahn istaz...@gmail.com wrote: Or go all the way

Re: [R] why is this a factor?

go the nuclear-global-override route. -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting

Re: [R] First time r user

, self-contained, reproducible code. -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] First time r user

, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting

Re: [R] First time r user

for more info along those lines: http://cran.r-project.org/web/views/HighPerformanceComputing.html Best regards and again thank you for the help, Paul El 18/08/2013 02:35, Steve Lianoglou lianoglou.st...@gene.com escribió: Hi Paul, First: please keep your replies on list (use reply-all

Re: [R] First time r user

so much Steve. The computer I'm currently working with is a 32 bit windows 7 OS. And RAM is only 4GB so I guess thats a big limitation. El 18/08/2013 03:11, Steve Lianoglou lianoglou.st...@gene.com escribió: Hi Paul, On Sun, Aug 18, 2013 at 12:56 AM, Paul Bernal paulberna...@gmail.com

Re: [R] How to extract last value in each group

and insidious adversary and taking steps to ensure you are getting what you want (whether using an index on a data.table, or some combo of split + max/which.max) probably is a good way to go. My 2 cents, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology

Re: [R] How to extract last value in each group

for the heavily degraded performance you're observing... our R data.table versions also match. -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch

Re: [R] How to extract last value in each group

-project.org/cgi-bin/mailman/listinfo/datatable-help -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read

Re: [R] How to vectorize subsetting

package: http://plyr.had.co.nz And read through this relevant chapter in Hadley's book: https://github.com/hadley/devtools/wiki/functionals#data-structure-functionals It will take you through looping, to *apply-ing, to plyr-ing HTH, -steve -- Steve Lianoglou Computational Biologist Bioinformatics

Re: [R] How to extract last value in each group

mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology

Re: [R] How to extract last value in each group

Or with plyr: R library(plyr) R ans - ddply(x, .(Date), function(df) df[which.max(df$Time),]) -steve On Wed, Aug 14, 2013 at 2:18 PM, Steve Lianoglou lianoglou.st...@gene.com wrote: While we're playing code golf, likely faster still could be to use data.table. Assume your data

Re: [R] ifelse() applied on function

me out. How about something like: loop - if (ChooseFn) lapply else sfLapply result - loop(MyList, function(x) { ## ... }) Should work as long as `sfLapply` has same function signature as lapply. HTH, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational

Re: [R] Advice on use of R for Generalised Linear Modelling

can try that. HTH, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R

Re: [R] Off-topic? Linux laptop for R

-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch

Re: [R] glmnet inclusion / exclusion of categorical variables

/gglasso/ Unfortunately it doesn't look like any of them support the equivalent of family=multinomial, only 2-class classification. HTH, -steve -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech __ R-help@r

Re: [R] Why is mclappy slower than apply in this case?

, self-contained, reproducible code. -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http

Re: [R] tree in tree package - Error: cannot allocate vector of size 2.0 Gb

) and monitor the R process as it's running, I reckon that's what you'll see, too. HTH, -stee -- Steve Lianoglou Computational Biologist Bioinformatics and Computational Biology Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch

Re: [R] ecdf --- title suggestion and question

=) R plot(ee, main=NULL) -steve -- Steve Lianoglou Computational Biologist Department of Bioinformatics and Computational Biology Genentech __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide

Re: [R] SVD on very large data matrix

provides a fast way to compute partial singular value decompositions (SVD) of large matrices ... HTH, -steve -- Steve Lianoglou Defender of The Thesis | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] Elasticnet - Cross validation problem

case -- I guess you would reduce your feature matrix for that fold, run the goods, then drop the coefs back into the original columns they'd belong to as if you ran the training on the full feature matrix. Know what I mean? HTH, -steve -- Steve Lianoglou Defender of The Thesis | Memorial Sloan

Re: [R] loop in a data.table

into an email that reconstructions a small version of your data.table (maybe 5-10 columns and one or two groups) it'd be more clear for me. Thanks, -steve -- Steve Lianoglou Defender of The Thesis | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info

Re: [R] scan not working

]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems

Re: [R] foreach takes foreever?

iteration is more involved, the benefit of parallelization will become more clear. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] (no subject)

a brief explanation (code would be helpful) of what you are trying to do? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] pROC and ROCR give different values for AUC

where things are going south. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R

Re: [R] Line numbers with errors and warnings?

/wiki/Konami_Code :-) -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted

Re: [R] Line numbers with errors and warnings?

to help you with). Also, emacs/ess also has tracebug: http://code.google.com/p/ess-tracebug/ which may be useful. anyway ... if you are leaving R for greener pastures, do us a favor and send us an email w/ an update if you find Nirvana in another language ;-) -steve -- Steve Lianoglou Graduate

Re: [R] Using multicores in R

to help, tho. -Steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted

Re: [R] Line numbers with errors and warnings?

will get better, so ... stay strong. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] Line numbers with errors and warnings?

: Le dimanche 02 décembre 2012 à 06:02 -0500, Steve Lianoglou a écrit : Hi, On Sun, Dec 2, 2012 at 12:31 AM, Worik R wor...@gmail.com wrote: What I mean is how do I get the R compilation or execution process to spit out a line number with errors and warnings? Indeed, I

Re: [R] aggregate() runs out of memory

Hi, On Tue, Nov 27, 2012 at 11:29 AM, Sam Steingold s...@gnu.org wrote: * Steve Lianoglou znvyvatyvfg.ubarl...@tznvy.pbz [2012-11-26 19:47:25 -0500]: [snip] It just occurred to me that this is even better: R setkeyv(f, c(share.id, delay)) R result - f[, list(min=delay[1L], max=delay[.N

Re: [R] GLM Coding Issue

, just trying to better understand. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] GLM Coding Issue

: the cbind-ing thing -Steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact [[alternative HTML version deleted

Re: [R] GLM Coding Issue

Hi Peter, On Tue, Nov 27, 2012 at 8:05 PM, Peter Ehlers ehl...@ucalgary.ca wrote: On 2012-11-27 14:34, Steve Lianoglou wrote: [snip] Steve: re a matrix response: see MASS (the book, 4ed) page 191; also found in the ch07.R file in the /library/MASS/scripts folder. I seem to recall

Re: [R] aggregate() runs out of memory

Hi Sam, On Mon, Nov 26, 2012 at 3:13 PM, Sam Steingold s...@gnu.org wrote: Hi, * Steve Lianoglou znvyvatyvfg.ubarl...@tznvy.pbz [2012-11-19 13:30:03 -0800]: For instance, if you want the min and max of `delay` within each group defined by `share.id`, and let's assume `infl

Re: [R] aggregate() runs out of memory

), I wonder if this two-step would be faster? R setkeyv(f, c('share.id', 'country')) R r1 - f[, list(min=min(delay), max=max(delay), count=.N), by='share.id'] R result - unique(f)[r1] ## I think -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering

Re: [R] aggregate() runs out of memory

://www.childpsy.net/ http://thereligionofpeace.com http://pmw.org.il http://honestreporting.com http://americancensorship.org Why do you never call me back after I scream that I will never talk to you again?! -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan

Re: [R] aggregate() runs out of memory

, you can do something like so: R as.data.table(infl) R setkey(infl, share.id) R result - infl[, list(min=min(delay), max=max(delay)), by=share.id] HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College

Re: [R] github

://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org

Re: [R] Stepwise regression scope: all interacting terms (.^2)

__ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student

Re: [R] history() does not work?

history in a file, so that I can choose from previous commands? The web did not throw up anything useful. Out of curiosity, when you call: R capabilities()['cledit'] Do you get `FALSE`? -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer

Re: [R] history() does not work?

On Wed, Oct 10, 2012 at 12:52 PM, Christian Hoffmann c-w.hoffm...@sunrise.ch wrote: Am 10.10.12 18:17, schrieb Steve Lianoglou: Hi, On Wed, Oct 10, 2012 at 12:03 PM, Christian Hoffmann c-w.hoffm...@sunrise.ch wrote: Hi, history() gives Error in savehistory(file) : no history available

Re: [R] Simple - Finding vector in a vector

- embed(x, e) ## Take a look at this matrix R r - apply(e, 1, rle) R sapply(r, function(rr) rr$lengths[1]) ## [1] 1 1 2 3 3 3 3 1 1 If your input vector (`x` here) is large, the call to `embed` may be painful. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology

Re: [R] Simple - Finding vector in a vector

Ugh, typo: On Mon, Oct 8, 2012 at 10:04 AM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: R x - c(NA, 1, NA, 1, 1, 1, 1, 1, 1, NA, 1) R e - embed(x, e) ## Take a look at this matrix R r - apply(e, 1, rle) R sapply(r, function(rr) rr$lengths[1]) ## [1] 1 1 2 3 3 3 3 1 1

Re: [R] R: machine for moderately large data

it is applicable in your case as well (in which case you might be able to rig up AWS to help you). HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http

Re: [R] How to write R package

. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing list

Re: [R] aggregate() runs out of memory

used plyr and data.table like stuff, so I might be missing your end goal -- providing a reproducible example with a small data.frame from you can help here (for me at least). HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center

Re: [R] $ operator is invalid for atomic vectors

for this error? I suspect you just have to ensure that the thing you are passing in to the `dataf2` parameter is in fact a data.frame -- the error you are getting suggests that it is currently not. Also -- have no fear for the space bar, it is your friend ;-) -- Steve Lianoglou Graduate Student

Re: [R] aggregate() runs out of memory

/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College

Re: [R] calcular SVD de una matriz que no entra en memoria

eventually do that myself. Hope that helps, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] latex \subfloat{} incompatible with sweave/knitr code

]{ \includegraphics[...]{figs/gen-someFig.pdf} } ... \end{figure} does the trick for me. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] A LaTeX question -- Hope people won't mind

...} HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact __ R-help@r-project.org mailing

Re: [R] Opinion: Why I find factors convenient to use

they save space over characters -- I believe that this is no longer true, but I'm not certain. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos

Re: [R] r data structures

='hello', c=matrix(1:100, nrow=10)) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] extended R

: http://cran.r-project.org/web/packages/RInside/index.html Keep in mind that R is released under the GPL, so depending on what your end game is for your software (are you making a commercial product?), this may or may not be an issue for you. -steve -- Steve Lianoglou Graduate Student

Re: [R] Help for Fisher's exact test

]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou

Re: [R] handle large matrix in R

http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact Info: http

Re: [R] Need Help in K-fold validation in Decision tree

a presentation of caret: http://files.meetup.com/1542972/Max_caret_NYCPA.pdf HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] pass objects into ... (dot dot dot)

(...) cat(There are, length(args), items passed in here\n) } R howMany(1, 2, 3, 4) There are 4 items passed in here R howMany(10, list(1:10)) There are 2 items passed in here -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center

Re: [R] pass objects into ... (dot dot dot)

: do.call(interval_intersection, my.interval.list) yay/nay? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] range segment exclusion using range endpoints

PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University

Re: [R] package ‘adehabitat’ is not available (for R version 2.15.0) on Mac OS X

]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve

Re: [R] Barplots inside loop - several data errors, workaround needed

of trying something There is a chance it might result in an error No error occurred while trying something ~ Does that help? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University

Re: [R] How to replace NA with zero (0)

example code, so this suggestion is far more general, but you might try something along the lines of: x[which(is.na(x))] - 0 Random note from left field: the call to `which` is unnecessary here. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering

Re: [R] rbind-ing numeric matrices

these objects in your workspace and copy/paste the output of dput on your m1 and m2 matrices so we can easily work w/ them. Cheers, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact

Re: [R] Why does my R compiler repeat my program whenever it is compiled?

@r-project.org javascript:; mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems

Re: [R] kernlab kpca code

do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University

Re: [R] Merge function - Return NON matches

-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos

Re: [R] Merge function - Return NON matches

. __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems Biology

Re: [R] R shell script

and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] R shell script

the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact Info

Re: [R] On the Design of the R Language

would be a better place to post such UN-expert opinion? I didn't realize you were also an expert on foreign affairs? Nice. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact

Re: [R] [BioC] Overlay Gene Expression on SNP (copy number) data

the vignettes of the following packages to see which one might suit you best: * Gviz * ggbio * GenomeGraphs -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org

Re: [R] How to take ID of number 7.

guess you probably figured that out by now, but just wanted to point that out. HTH, -steve On Sun, Apr 22, 2012 at 4:05 PM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: On Sun, Apr 22, 2012 at 7:03 AM, Yellow s1010...@student.hsleiden.nl wrote: I figured out something new that I would

Re: [R] How to take ID of number 7.

thise ID numbers also? Seems like there were already a few suggestions in this thread, but I'm surprised no one has suggested the use of `subset` yet, see ?subset: R interesting - subset(DataFile, log2 = 7)$ID Now play with the `interesting` data.frame to get the data you need -steve -- Steve

Re: [R] PCA sensitive to outliers?

deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve

Re: [R] Reading first line before using read.table()

something like this do? R title.line - readLines('file.rta', n=1) R dat - read.table('file.rta', skip=1, header=TRUE, ...) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact

Re: [R] SVM. How to use categorical attributes?

PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell

Re: [R] SVM. How to use categorical attributes?

not 100% sure they have what you're looking for, but as I said ... it's worth checking out. -steve On Wed, Mar 28, 2012 at 9:54 AM, Steve Lianoglou mailinglist.honey...@gmail.com wrote: Hi, These suggestions still require you to explicitly compute your feature space or kernel matrix first

Re: [R] lasso constraint

) of the model you are building, then it's time to pull yourself away from the keyboaRd and start doing some reading, or (as Bert will likely tell you) consult your local statistician. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center

Re: [R] installing R 2.14.2

the installation process the error occurs. Thanks, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact

Re: [R] SVM. How to use categorical attributes?

word appears). You can maybe get smarter and try to group like words together, but ... now you'll have two problems ... Hope you have lots of data! -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College

Re: [R] Convex optimization in R ?

. This is probably a good place for you to start looking: http://cran.r-project.org/web/views/Optimization.html HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology  | Memorial Sloan-Kettering Cancer Center  | Weill Medical College of Cornell University Contact Info: http

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