Re: [R] Debug

ws an error, it will be caught and stored in the result variable. In this case, the file.name will be written to your workspace. Instead of just printing to your workspace, you could consider storing the bad file names in a list and post-process later. Hope that helps, -steve

Re: [R] AsciiDoc and R

distribution for Max OS X? Perhaps this might help, too: http://learnr.wordpress.com/2009/09/29/wordpress-blogging-with-r-in-3-steps/ -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact

Re: [R] How can I avoid a for-loop through sapply or lapply ?

;hsa-miR-17" [10] "hsa-miR-18a" ... [888] "hsa-miR-675*" [889] "hsa-miR-888*" [890] "hsa-miR-541*" pieces <- strsplit(nml, " ")

Re: [R] C++

ing R Extensions" manual: http://cran.r-project.org/doc/manuals/R-exts.html#System-and-foreign-language-interfaces Also available in PDF: http://cran.r-project.org/doc/manuals/R-exts.pdf -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Ketter

Re: [R] How to sort the elements in a matrix?

ements in column 2, by the sequence of the elements in column 1 in ascending order? R> ab[order(ab[,1]),2] [1] 3 4 2 1 -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University

Re: [R] Working around 256 byte variable names? + trouble opening large file

not an excel guru, so I don't know how it handles data export when certain cells are missing in a row -- each row should have as many demarcated data points as any other. So if its a CSV, there should be just as many ","'s in line 397 as there are in the preceding lines

Re: [R] Any concept of 'by reference' or 'address of' in R?

lements in the matrix/data.frame, then you shouldn't have to worry, and look to optimize elsewhere ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio

Re: [R] Emacs and ESS help

directory which emacs will find. The "~" abbreviation is required and is interpreted to be your home directory. In emacs C-x C-f ~/.emacs And for what it's worth "~" translated to C:\Documents and Settings \YOURACCOUNT on your windows box ... I think. -steve --

Re: [R] R on browser

e happy to help. 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 __ R-hel

Re: [R] Updating R-code in own package

find anything about updating R-code in the package. I'm pretty sure the only "correct" thing to do is just fix the code in your package's source tree then reinstall the package wholesale to replace the bad code with the fixed code. -steve -- Steve Lianoglou Graduate Stude

Re: [R] SVM

learning more about SVMs and other machine learning approaches, you can watch Andrew Ng's intro to machine learning classes online. The relevant links are at the top of this page: http://ai.stanford.edu/~ang/courses.html -steve -- Steve Lianoglou Graduate Student: Computational Systems B

Re: [R] SVM

? I'm not really sure where to begin ... what are you trying to do, exactly? Why do you think you want to build an SVM? What do you expect it to do for you? -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical Co

Re: [R] SVM

the Examples section of ?svm .. it's pretty straight forward. Let us know what problems you're having understanding those examples and we can try to offer some insight. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Cente

Re: [R] T-test to check equality, unable to interpret the results.

han measured: sorry. Thanks for wearing the stats prof hat, though. It's good that someone stepped up to lay down the law. With white flag raised, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College

Re: [R] T-test to check equality, unable to interpret the results.

he p- value (in any statistical test), the less confident you should be that rejecting the null hypothesis is a good idea. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University

Re: [R] Turnpoints

ave count less than 4000 2. You can use it to select out of the vector. R> df[less4000,] You can also use the subset function R> subset(df, count < 4000) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill

[R] Putting together a constantly evolving package

ight do eventually down the road, anyway), but I'm wondering if there are other alternatives. Thanks, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info:

Re: [R] identical(length(x), 1) returns FALSE, but print(length(x)) is 1, length(x)==1 is TRUE, and is.integer(lenght(x)) is TRUE????

), 1L) is TRUE ... ouch ... I guess the lesson learned is that: identical() != == -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] Boost in R

mcr: 0 achieved after 20 boosting step(s) What is "mcr" mean? Third link down: http://www.google.com/search?hl=en&q=logitboost+mcr&spell=1 Looks like MCR == misclassification rate? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial S

Re: [R] Is there an equivalent of "echo"

hz.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 | Memorial Sloan-Kettering Cancer Center | Weill Medica

Re: [R] Strange question/result about SVM

t then it just seems to look like line noise ... infer them as you see fit ... -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: ht

Re: [R] average for files and graph

type of plot do you expect to see? ?plot ?barchart ?barplot ?boxplot ?points ?lines ... -- 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/co

Re: [R] (no subject)

Hi, On Sep 14, 2009, at 10:19 AM, asie soheili wrote: I want to comput prime component of a graph. please guide mi. If you're working with graphs, you'll want to check out the igraph package: http://cran.r-project.org/web/packages/igraph/ http://igraph.sourceforge.net/ -steve

Re: [R] Eliminate cases in a subset of a dataframe

them). Refer to them by their position in the data.frame as you would if you didn't create a subset. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell Universit

Re: [R] call for input

e. See: ?readline -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-pro

Re: [R] 64-bit OSX binary for 2.9.2

acked in the root (e.g. tar fvxz R*.tar.gz -C /), but doesn't contain the GUI (see below for a separate download).""" You'll have to install the R.app GUI separately if you want to use the 2.9.2 install, otherwise I think the 2.9.0 *.pkg installer includes

Re: [R] Location of Packages?

s. 32 bit, look at the size of the pointer: R> .Machine$sizeof.pointer [1] 8 8 means 64 bit, 4 means 32 bit. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info:

Re: [R] linear regression, exclude a datum

doesn't make sense to you, please post some code we can comment on. -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/~l

Re: [R] Way to iteratively change line color and line style

Hi, On Fri, Sep 11, 2009 at 8:12 PM, Jason Rupert wrote: > I would like to have a way to automatically change the line color and line > style. For auto-generating colors, try ?rainbow Not sure about what you can do about alternating the line style ... -steve -- Steve Lianoglou Gr

Re: [R] help with for loop

each row of your matrix, yes? Look at the ``apply`` function, with MARGIN set to 1. Here I'm just calling the ``mean`` function over every row of my matrix: R> m <- matrix(1:100, 10, 10) R> apply(m, 1, mean) [1] 46 47 48 49 50 51 52 53 54 55 Substitute your own function f

Re: [R] Moving to Mac OS X

R.app GUI, you can get it from here: http://r.research.att.com/#GUI For some reason the 2.9-leopard.dmg is missing (though the 2.10-devel is there). This was just noticed on R-sig-mac earlier today and, AFAIK, it should be back soon. -steve On 9/11/09 12:38 PM, Steve Lianoglou wrote:

Re: [R] Moving to Mac OS X

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 | Memorial Sloan-Kettering

Re: [R] help with plotting

ou see how length(a) > 1 -- what should ``if (a)`` evaluate to? R is telling you that it's just evaluating a[1]. So, maybe your data isn't what you expect it to be? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center

Re: [R] Working with large matrix

the lm. I am using LINUX 64 bit with 32G mem. Is there an elegant and fast way of completing this task? Do bigmemory and biglm help? http://cran.r-project.org/web/packages/bigmemory http://cran.r-project.org/web/packages/biglm -steve -- Steve Lianoglou Graduate Student: Computational Systems

Re: [R] Moving to Mac OS X

at's all I really need as I spend most of my time in the terminal then sourcing some file that has the functions I'm trying to refine anyway ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Me

Re: [R] transposing a distance matrix in R

o now: R> who.vs.who[lower.tri(m),] Var1 Var2 2BA 3CA 6CB ... almost there, no just put it together: R> dist <- m[lower.tri(m)] R> who <- who.vs.who[lower.tri(m),] R> names(dist) <- paste(who[,1], who[,2], sep=".vs.") R> dist B.vs.A C.vs.A

Re: [R] Graph visualization

) mat <- rbind(c(0, 0, 1, 1), c(0, 0, 1, 1), c(1, 1, 0, 1), c(1, 1, 1, 0)) dimnames(mat) <- list(LETTERS[1:4], LETTERS[1:4]) graph <- graph.adjacency(mat) tkplot(graph) (you can specify different layouts, too). HTH, -steve -- Steve L

Re: [R] memory limit problem

er 16384*16384 > Error: cannot allocate vector of size 512.0 Mb > I not have other objects in R memory. > what I do? Get a 64 bit system and ditch windows? http://thread.gmane.org/gmane.comp.lang.r.general/64637 Or maybe the bigmemory package can help? http://cran.r-project.org/web/packages

Re: [R] Linux R version: best?

the latest version when it's released. -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/co

Re: [R] Regarding SVM using R

replies on list 2 . Please post your new code along with the error. Thank, -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] Regarding SVM using R

t. In short -- stop removing the features (columns) from your training/ testing data and it should work. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskc

Re: [R] sparse vectors

ng-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/contact ___

Re: [R] Regarding SVM using R

from your validation set when you pass it into the predict function? ie: predict(model.ksvm, validation[, -length(validation)] should probably be predict(model.ksvm, validation, ...) That should work ... but if you're using this for anything serious, be sure you understand why.

Re: [R] About " create dataset permanently in package "

nd Settings\YOU\RainRainGoAway \rain1.rda", then load it from there in R: R> load("C:\Documents and Settings\YOU\ RainRainGoAway\rain1.rda") That should do the trick ... let us know if you need more help. -steve -- Steve Lianoglou Graduate Student: Computational Syste

Re: [R] OT - Banker's Algorithum

on below to R: http://en.wikipedia.org/wiki/Banker%27s_algorithm#Pseudo-Code.5B3.5D Not really sure what else to say ... for instance, the line: P = P - {p} Might be: P <- setdiff(P, p) Maybe use lists to hold the stuff in P? Don't know what else you're looking for ... -steve -- Steve Lianoglo

Re: [R] Averaging rows if a condition is true.

oblems using it, please post a small representative matrix of your data that we can paste into our own R session to slice and dice for you as an example. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of C

Re: [R] get the command line

On Mon, Sep 7, 2009 at 12:00 AM, Peng Yu wrote: > On Sun, Sep 6, 2009 at 10:50 PM, Steve > Lianoglou wrote: >> Hi, >> >> On Sun, Sep 6, 2009 at 11:25 PM, Peng Yu wrote: >>> Hi, >>> >>> commandArgs gives me the arguments. I am wondering what comm

Re: [R] get the command line

(), collapse=" ") Can you give an example of what you're trying to get? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info:

Re: [R] how do I draw this surface -- hand drawn in the attachemtn

y seen it in actio in the lattics vs. ggplot series of posts on the learnr.wordpress.com blog (very helpful). -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http

Re: [R] Color index in image function

= terrain.colors(100), axes = FALSE) Right here: R> terrrain.colors(100) [1] "#00A600FF" "#03A700FF" "#07A800FF" "#0AAA00FF" "#0EAB00FF" ... Is that what you mean? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Mem

Re: [R] using histogram to find cdf

Hi, On Sun, Sep 6, 2009 at 7:03 AM, maram salem wrote: > Dear all, > How can I use the histogram density estimate (hist) to find the value of the > cdf at a certain point? Can you just use the ecdf function on your original data? -steve -- Steve Lianoglou Graduate Student: Comp

Re: [R] About BIC

I just ran ??bic to find it. 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] Regarding SVM using R

ries to send a sql query to your database and will be returned a data.frame of your results. You can manipulate that data.frame in the usual way to pick off your "target" column from. the predictor/feature columns and train your SVM accordingly (or use the entire data.frame along with the for

Re: [R] foreach + snowfall for multicore situations

over using the foreach w/ multicore backend? Just curious because I've moved off of any snow* related packages since I only parallelize on the same box and find that the foreach/ doMC combo works just fine. -steve -- Steve Lianoglou Graduate Student: Computational Systems Bi

Re: [R] how to save an updated dataset

elp@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 | Memori

Re: [R] Loading file in MAC-Syntax Error

sktop/test.txt/ 1. Where's your code? 2. Try to remove the trailing slash of your filename > It always gives me Syntax error message. What is the error message? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill

Re: [R] SVM coefficients

ich is already implemented for you in the penalized svm package (haven't used it myself): cran: http://cran.r-project.org/web/packages/penalizedSVM/index.html publication: http://bioinformatics.oxfordjournals.org/cgi/content/full/25/13/1711 Does that help? -steve -- Steve Lianoglou Gra

Re: [R] Calling C funtion from R help Needed

ll would be: .C('checkstr_R_wrapper', n=as.character(n), n_length=length(as.character(n)), m=as.integer(m), result=integer(1)) ... or something ... perhaps. Does that help any? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sl

Re: [R] SVM coefficients

ing. SVMs are great for accuracy, but notoriously hard for interpretation. To try and squeeze some interpretability from your classifier in your feature space, you might try to look at the weights over your w vector: http://www.nabble.com/How-to-get-w-and-b-in-SVR--%28package-e1071%29-td24790413

Re: [R] SVM coefficients

uot; attribute, which I guess is what you're looking for (?) Run "example(svm)" to its end and type: R> m$coefs [,1] [1,] 1.00884130 [2,] 1.27446460 [3,] 2. [4,] -1. [5,] -0.35480340 [6,] -0.74043692 [7,] -0.87635311 [8,] -0.04857869 [9,

Re: [R] find numbers in a line with letters

t;, perl=T) [[1]] [1] 17 47 attr(,"match.length") [1] 4 5 R> gregexpr("(\\d+(\\.\\d+)?)", "this Item costs 3.32 Dollars, that item costs 10 dollars even, ", perl=T) [[1]] [1] 17 47 attr(,"match.length") [1] 4 2 R> gregexpr("(\\d+(\\.\\d+)?)&

Re: [R] rJava error for large XML object return in StatET plugin

Hi, On Aug 26, 2009, at 1:31 PM, Harsh wrote: Hi R List, I get this error using StatET R plugin in Eclipse. You might have more luck asking the StatET user mailing list: https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/statet-user -steve -- Steve Lianoglou Graduate Student

Re: [R] GLMs

neralized mixed model") Will provide many answers. -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] Filtering matrices

ntersection, take an & of the two vectors, # but this is empty in this case. Either way, this would get # the points you're after my.data[good.cor & good.p] Does that make sense? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering C

Re: [R] Filtering matrices

e three small example matrices and let us know what you'd like your indexing to return. Someone will provide the code to show you the correct way to do it. HTH, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical Co

Re: [R] Help on comparing two matrices

graph.isomorphic(g1, g2) # Or, using the (somehow fast) vf2 algorithm is.iso <- graph.isomorphic.vf2(g1, g2) 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] Help on comparing two matrices

can pad your matrices with zero rows or columns (depending on what's deficient) as an easy way out. Just an idea. Of course, if David's solution is what you need, then no need to bother with any of this. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology

Re: [R] Help on comparing two matrices

columns to a sorted matrix. > If you want to go about this by implementing the algo you described, I think > you'd be best suited via some divide-and-conquer/recursion route: Starting from step 2, that is. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Me

Re: [R] Help on comparing two matrices

ttp://en.wikipedia.org/wiki/Divide_and_conquer_algorithm Perhaps you can take inspiration from some concrete sorting algorithms that are implemented this way: Merge sort: http://en.wikipedia.org/wiki/Merge_sort Quick sort: http://en.wikipedia.org/wiki/Quicksort Hope that helps, -steve -- S

Re: [R] computation of matrices in list of list

) [,1] [,2] [,3] [,4] [,5] [1,] 5.003219 2.2498521 2.9065183 -2.7294155 5.5118195 [2,] 1.560042 -2.0677467 -1.5175750 3.1384472 1.7245805 [3,] -4.653988 -0.8043570 -1.3420022 -5.6794115 0.5077933 [4,] -7.433055 0.8248184 -0.8724350 -0.2229058 -3.7149176 [

Re: [R] extra .

s any insight into that. I've always been curious and I seem to see it done in many different functions and packages, so I feel like I'm missing something ... Thanks, -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kette

Re: [R] Convert list to data frame while controlling column types

RUE Can you check to see if your data's wonky somehow? -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] LASSO: glmpath and cv.glmpath

;t don't do them)[1] ... you might want to further divide your data into training/tuning/test (somewhere between steps 1 and 2) as another means of scoring models. HTH, -steve [1] http://hunch.net/?p=29 -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Slo

Re: [R] a naive question

n, like so R> x[,1] You can use that to plot a histogram of the numbers in the first column: R> plot(hist(x[,1])) -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contac

Re: [R] Erros with RVM and LSSVM from kernlab library

b=1:10) R> is(df) [1] "data.frame" "list" "oldClass" "mpinput""vector" But R> is(df, 'list') [1] FALSE So, in short, I don't know if that's what's happening ... did it fix your problem, tho? -steve

Re: [R] Erros with RVM and LSSVM from kernlab library

ather than the matrix which you think you're passing in. Does that do the trick? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: h

Re: [R] Erros with RVM and LSSVM from kernlab library

therwise, can you provide something of a self- contained piece of code that you're using to invoke these functions such that it's giving you these errors? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill

Re: [R] Tr : create a table in the console!!

t understand what you want to do. From the code you've pasted, you already have extracted the numbers you wanted, so what do you mean when you say "I want to do a table" with them? Do you just want to put them in a data.frame, or something? -steve -- Steve Lianoglou Grad

Re: [R] open txt

oblema Tu file "plantula.txt" no esta aqui (I think). In short: you are passing some function the name of a file that doesn't exist. Try passing the absolute path to the plantula.txt file to your call to ``file()`` -steve -- Steve Lianoglou Graduate Student: Computational

Re: [R] value of nth percentile

the R code or command for this please let me know. I would appreciate your early response. R> dat <- rnorm(100, mean=10, sd=2) R> quantile(dat, .9) 90% 12.53047 R> sum(dat < quantile(dat, .9)) / length(dat) [1] 0.9 -steve -- Steve Lianoglou Graduate Student: Computational

Re: [R] Newbie that don't understand R code

*t))/2) out } ) phi.inverse( - log(U)/Y, theta) phi.inverse was defined as the function returned by the switch statement. ``- log(U)/Y`` is passed in to the function's ``t`` argument. Does that help? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology |

Re: [R] lm.fit algo

ctor * ~ is used as "almost equals") You'll need some numerical/scientific/matrix library in java, perhaps this could be a place to start: http://commons.apache.org/math/userguide/stat.html#a1.5_Multiple_linear_regression Hope that helps, -steve -- Steve Lianoglou Graduate St

Re: [R] Remove columns

om the result. -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-proje

Re: [R] printing a dataframe summary to disk

rame) write.table(my.summary, quote=FALSE, file="summary.txt") -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info:

Re: [R] Replacing NA values in one column of a data.frame

_ 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: C

Re: [R] creating list of the from 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, . . ., n, n, n?

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 __ R-help@r-project.org mailing l

Re: [R] Coding problem: How can I extract substring of function callwithin the function

ou *might* be doing in the short term. Then again, it might not be. Everyone has their own style of teaching, and it's your prerogative to do it as you see fit. I wouldn't presume to know which way is best, so good luck with the upcoming semester :-) -steve -- Steve Lian

Re: [R] Coding problem: How can I extract substring of function callwithin the function

me. But if you're trampling over some base:: function for something trivial like changing the value of one default parameter to something else, you might as well just get them to learn how to use the ? asap as well. -steve -- Steve Lianoglou Graduate Student: Computational Systems Bio

Re: [R] request: Help

-- 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 https

Re: [R] Nominal variables in SVM?

lor and height, your "feature matrix" for N examples would be N x 4 0,1,0,15 # blue object, height 15 1,0,0,10 # red object, height 10 0,0,1,5 # green object, height 5 ... -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer

Re: [R] problem loading ncdf library on MAC

get the required libs and try again. Or are you getting different errors? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: ht

Re: [R] logged2

r package, but nothing else. If you can let us know where you're seeing this function used, we could likely provide more help. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornel

Re: [R] R help from command line

ention, but are you working on a machine with a windowing system + browser? If so, set your help files to be seen in the browser: R> option(htmlhelp=TRUE) next time you ask for some ?help, it should pop up a browser window. Good enough? -steve -- Steve Lianoglou Graduate Student: Com

Re: [R] problem selecting rows meeting a criterion

OK so the lesson so far is "use the subset function". Hopefully you're learning a slightly different lesson now :-) Does that clear things up at all? -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center

Re: [R] howto get the number of columns and column names of multiply data frames

put of ls() into a list also does not work. How can I accomplish this task?? If you still want to do it this way, see: ?get for example: for (varName in paste('dataframe', 1:n, sep='')) { cat(colnames(get(varName))) } HTH, -steve -- Steve Lianoglou Graduate Student: C

Re: [R] using cat()

You can use cat *in* a function to print the value of a variable, but you can't "reach into" a function to pull out a variable's value. Are you trying to debug something? See: ?debug to step through a function to examine what it's doing one step at a t

Re: [R] Ylim

ylim = c(Ymin,Ymax) ) segments(Graph, dat$SM + dat$E, Graph, dat$SM - dat$E) i <- i + 3 j <- j + 1 } dev.off() And the error message is: Error in plot.window(xlim, ylim, log = log, ...) : invalid 'ylim' value Calls: barplot -> barplot.default -> plot.window E

Re: [R] A question regarding R scoping

such: f1 <- function(i) assign('i', 10, envir=parent.frame()) f2 <- function(n) { i <- length(n) f1(i) print(i) } R> f2(1:20) [1] 10 Honestly, this just smells like a *really* bad idea, though ... just have f1() return a value that you use in f2. -steve -- Steve

Re: [R] calasification table under conditions

use some regular expression mojo: dat <- read.csv2(...) tab1 <- dat[grep('[ABCD]', dat[,2], ] tab2 <- dat[grep('[EFGH]', dat[,2]), ] optionally rm the dat variable if you're hurting for RAM. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology

Re: [R] making scatter plot points fill semi-transparent

> rgb(red=0, green=0, blue=255, alpha=10, max=255) [1] "#FF0A" R> plot( rnorm(1000), rnorm(1000), col="#FF0A", pch=16,cex=3) is there any way to pass in the usual col="colorname" argument and then tweak that color's transparency? Maybe, but I&#

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