Re: [R] Hello,
Kiran exonmap is a bioconductor package - I'd suggest trying the bioconductor mailing list. Also, you're more likely to get a response if you include an informative subject line. Regards Richard. Kiran Annaiah wrote: Hello, A newbie to R. I am trying to use the exonmap package in R. According to the docs, the xmapDatabase() command should read the config file with all the connection parameters and connect to the DB. But i get the error shown below xmapDatabase(Human) Error in mysqlNewConnection(dbDriver(drv), ...) : RS-DBI driver: (could not connect [EMAIL PROTECTED] on dbname NA Error:Access denied for user 'cagadmin'@'cdev.cag.chop.edu' to database 'NA' ) when i connect to db using dbConnect() it works fine. conn-dbConnect(drv=MySQL,username=cagadmin ) Anybody who can shed some light on whats going on here? thank you all kiran Kiran Annaiah Center for Applied Genomics Informatics Children's Hospital of Philadelphia 267-426-9355 __ 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. -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
Re: [R] rpart confidence intervals?
Hi RichardP I guess you'll increase your chances of a response if you include some affiliation info. This could also avoid getting you confused with other people - I thought for a minute I'd been sleep-emailing :-) Cheers A N Other RichardP RichardP wrote: hi, I am using rpart with a continuous response variable. Is there a way to extract 95% confidence intervals for the predicted mean at each node? cheers. -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
Re: [R] Error in installing packages
Lazarus I'm not sure your first problem is actually a problem - it looks to me like the epicalc package installed OK. Have you tried using epicalc? I'm sure your problem 2 is not an R problem, so don't know whether you'll get any help on this list. Best wishes Richard. Lazarus Mramba wrote: Dear R Users; I am an R user who has recently bought a new laptop;Toshiba Satellite U405 running on both Windows Vista and Ubuntu. I have problems on the wondows vista when installing packages. The argument 'lib' is missing. How do i solve this problem? Illustration: install.packages(epicalc) Warning in install.packages(epicalc) : argument 'lib' is missing: using 'C:\Users\lazurus\Documents/R/win-library/2.7' --- Please select a CRAN mirror for use in this session --- trying URL 'http://cran.za.r-project.org/bin/windows/contrib/2.7/epicalc_2.7.1.2.zip' Content type 'application/zip' length 629215 bytes (614 Kb) opened URL downloaded 614 Kb package 'epicalc' successfully unpacked and MD5 sums checked The downloaded packages are in C:\Users\lazurus\AppData\Local\Temp\RtmpMrOxin\downloaded_packages updating HTML package descriptions ## problem 2 is about downloading R without internet connection I have failed to get internet working under ubuntu for both wireless LAN and Ethernet cable and therefore i cannot download R from the net. Both wireless and ethernet are not detected at all leave alone connecting to the internet. I am using Atheros AR5007EG wireless network adapter, Marvel Yukon 88E8040T PCI-E Fat Ethernrt Controller. Internet works fine under the windows Vista system but not on the Ubuntu side Anyhelp will be appreciated. Kind regards, Lazarus Mramba Junior Statistician P.O Box 986, 80108, Kilifi, Kenya Mobile No. +254721292370 Tel: +254 41 522063 Tel: +254 41 522390 (office extension : 419) __ 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. -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
Re: [R] Creation of png=problems
Romain You might get a fuller answer from others, but one thing you could try is using bitmap() rather than png(). Cheers Richard. Romain wrote: Hi everybody, I am currently working with R and I would like to create jpeg graphs with it. I am working on Windows and Unix but I would like to be able to create graphs (jpeg, png, bitmap...) under Unix. I am working on Solaris version 8. The documentation for R states that the latest version of or R known to compile on Solaris 8 is version 2.6.2. I have been able to compile and install R version 2.6.2. under Unix. I also installed Hmisc package needed by my script. The problem is that when I launch my script to create graphs from text files I get this error : Create_Graph(File) Error in X11(paste(png::, filename, sep = ), width, height, pointsize, : unable to start device PNG In addition: Warning message: In png(paste(PATH, /, filename, sep = ), 800, 600) : no png support in this version of R The thing is that I have tried to run my script under Windows with the same version (2.6.2) and everything is going well and the graph are created. Is it because (under Unix): capabilities() jpeg pngtcltk X11 http/ftp sockets libxml fifo FALSEFALSEFALSE TRUE TRUE TRUE TRUE TRUE If so, could someone explain to me how to change these capabilities in order to ba able to set them TRUE. I have also tried with other version of R but the error is the same one. If you have any other ideas about why it doesn't work I would be very grateful. The fact is that I have created a programm under Unix to make automatic the creation of the text files and I would like to create automatically the correspondant graphs. I hope someone will be able to help me. Thanks for your time. Have a good day. R. La route des vacances en quelques clics grâce à Voila ! http://itineraire.voila.fr/itineraire.html __ 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. -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
[R] Subsetting an array by a vector of dimensions
Hi Is it possible to subset an n-dimensional array by a vector of n dimensions? E.g. assume I have x - array(1:24, dim=2:4) x[1,1,2] [1] 7 dims - c(1,1,2) I would like a function that I can supply x and dims as parameters to, and have it return 7. Also, I would like to do something like: x[1,1,] [1] 1 7 13 19 dims2- c(1,1,NA) And have a function of x and dims2 that gives me back [1] 1 7 13 19 Does such a thing exist? Thanks Richard -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
Re: [R] Subsetting an array by a vector of dimensions
My understanding of matrix subscripting is that this can be used to access
arbitrary elements from an array and return them as a vector, but I don't
understand how that helps me here. I've now written a function that seems to do
what I originally wanted, but I've also realised I want to do assignment too. I
need to read up more on writing assignment functions to do this. However, I'm
thinking that someone has already solved this, in a far more elegant way than
my hacking :-). Here's my function for anyone interested:
subsetArray - function(x, subset) {
+ subsetString - paste(subset, collapse=,)
+ subsetString - gsub(NA,,subsetString)
+ evalString - paste(expression(x), [, subsetString, ])
+ eval(parse(text=evalString))
+ }
x - array(1:24, dim=2:4)
subsetArray(x, c(1,1,2))
[1] 7
subsetArray(x, c(1,NA,2))
[1] 7 9 11
subsetArray(x, c(1,NA,NA))
[,1] [,2] [,3] [,4]
[1,]17 13 19
[2,]39 15 21
[3,]5 11 17 23
subsetArray(x, c(1,1,2)) - 25
Error in subsetArray(x, c(1, 1, 2)) - 25 :
could not find function subsetArray-
Best wishes
Richard.
Patrick Burns wrote:
I think you are looking for subscripting with a
matrix:
x[cbind(1,1,2)]
See, for instance, the subscripting section of chapter 1
of S Poetry.
Patrick Burns
[EMAIL PROTECTED]
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and A Guide for the Unwilling S User)
Richard Pearson wrote:
Hi
Is it possible to subset an n-dimensional array by a vector of n
dimensions? E.g. assume I have
x - array(1:24, dim=2:4)
x[1,1,2]
[1] 7
dims - c(1,1,2)
I would like a function that I can supply x and dims as parameters to,
and have it return 7. Also, I would like to do something like:
x[1,1,]
[1] 1 7 13 19
dims2- c(1,1,NA)
And have a function of x and dims2 that gives me back [1] 1 7 13 19
Does such a thing exist?
Thanks
Richard
--
Richard D. Pearson [EMAIL PROTECTED]
School of Computer Science,http://www.cs.man.ac.uk/~pearsonr
University of Manchester, Tel: +44 161 275 6178
Oxford Road, Mob: +44 7971 221181
Manchester M13 9PL, UK.Fax: +44 161 275 6204
__
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.
Re: [R] Subsetting an array by a vector of dimensions
In case anyone's still interested, I now have (I think!) a complete solution
(thanks to a quick look at my new favourite document - S Poetry :-)
subsetArray - function(x, subset) {
subsetString - paste(subset, collapse=,)
subsetString - gsub(NA,,subsetString)
evalString - paste(expression(x), [, subsetString, ])
eval(parse(text=evalString))
}
subsetArray-- function(x, subset, value) {
subsetString - paste(subset, collapse=,)
subsetString - gsub(NA,,subsetString)
evalString - paste(expression(x), [, subsetString, ] -,
expression(value))
eval(parse(text=evalString))
x
}
x - array(1:24, dim=2:4)
subsetArray(x, c(1,1,2))
subsetArray(x, c(1,1,2)) - 25
x
Thanks to Pat!
Richard
Richard Pearson wrote:
My understanding of matrix subscripting is that this can be used to
access arbitrary elements from an array and return them as a vector, but
I don't understand how that helps me here. I've now written a function
that seems to do what I originally wanted, but I've also realised I want
to do assignment too. I need to read up more on writing assignment
functions to do this. However, I'm thinking that someone has already
solved this, in a far more elegant way than my hacking :-). Here's my
function for anyone interested:
subsetArray - function(x, subset) {
+ subsetString - paste(subset, collapse=,)
+ subsetString - gsub(NA,,subsetString)
+ evalString - paste(expression(x), [, subsetString, ])
+ eval(parse(text=evalString))
+ }
x - array(1:24, dim=2:4)
subsetArray(x, c(1,1,2))
[1] 7
subsetArray(x, c(1,NA,2))
[1] 7 9 11
subsetArray(x, c(1,NA,NA))
[,1] [,2] [,3] [,4]
[1,]17 13 19
[2,]39 15 21
[3,]5 11 17 23
subsetArray(x, c(1,1,2)) - 25
Error in subsetArray(x, c(1, 1, 2)) - 25 : could not find function
subsetArray-
Best wishes
Richard.
Patrick Burns wrote:
I think you are looking for subscripting with a
matrix:
x[cbind(1,1,2)]
See, for instance, the subscripting section of chapter 1
of S Poetry.
Patrick Burns
[EMAIL PROTECTED]
+44 (0)20 8525 0696
http://www.burns-stat.com
(home of S Poetry and A Guide for the Unwilling S User)
Richard Pearson wrote:
Hi
Is it possible to subset an n-dimensional array by a vector of n
dimensions? E.g. assume I have
x - array(1:24, dim=2:4)
x[1,1,2]
[1] 7
dims - c(1,1,2)
I would like a function that I can supply x and dims as parameters
to, and have it return 7. Also, I would like to do something like:
x[1,1,]
[1] 1 7 13 19
dims2- c(1,1,NA)
And have a function of x and dims2 that gives me back [1] 1 7 13 19
Does such a thing exist?
Thanks
Richard
--
Richard D. Pearson [EMAIL PROTECTED]
School of Computer Science,http://www.cs.man.ac.uk/~pearsonr
University of Manchester, Tel: +44 161 275 6178
Oxford Road, Mob: +44 7971 221181
Manchester M13 9PL, UK.Fax: +44 161 275 6204
__
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.
Re: [R] Sum(Random Numbers)=100
Shubha
Does table(ceiling(runif(100,0,50))) give you something like you want?
Richard.
Shubha Vishwanath Karanth wrote:
...actually I need to allocate certain amount of money (here I mentioned
it as 100) to a randomly selected stocks(50 stocks)... i.e., 100 being
divided among 50 stocks and preferably all are integer allocations(i.e.,
5 8 56 12 etc without any decimals)...
Thank you,
Shubha
-Original Message-
From: Moshe Olshansky [mailto:[EMAIL PROTECTED]
Sent: Tuesday, July 08, 2008 12:09 PM
To: [EMAIL PROTECTED]; Shubha Vishwanath Karanth
Subject: Re: [R] Sum(Random Numbers)=100
If they are really random you can not expect their sum to be 100.
However, it is not difficult to get that given that the sum of n
independent Poisson random variables equals N, any individual one has
the conditional binomial distribution with size = N and p = 1/n, i.e.
P(Xi=k/Sn=N) = (N over k)*(1/n)^k*((n-1)/n)^(N-k).
So you can generate X1 binomial with size = 100 and p = 1/50; if X1 = k1
then the sum of the rest 49 must equal 100 - k1, so now you generate X2
binomial with size = 100-k1 and p = 1/49; if X2 = k2 then generate X3
binomial with size = 100 -(k1+k2) and p = 1/48, etc.
Why do you need this?
--- On Tue, 8/7/08, Shubha Vishwanath Karanth [EMAIL PROTECTED]
wrote:
From: Shubha Vishwanath Karanth [EMAIL PROTECTED]
Subject: [R] Sum(Random Numbers)=100
To: [EMAIL PROTECTED]
Received: Tuesday, 8 July, 2008, 3:58 PM
Hi R,
I need to generate 50 random numbers (preferably poisson),
such that
their sum is equal to 100. How do I do this?
Thank you,
Shubha
This e-mail may contain confidential and/or privileged
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PLEASE do read the posting guide
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--
Richard D. Pearson [EMAIL PROTECTED]
School of Computer Science,http://www.cs.man.ac.uk/~pearsonr
University of Manchester, Tel: +44 161 275 6178
Oxford Road, Mob: +44 7971 221181
Manchester M13 9PL, UK.Fax: +44 161 275 6204
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] I want to install a package on Max OS X from a local file
From the (terminal window) command line try: R CMD INSTALL path.to.file/filename.tar.gz Does that do it? Richard stephen sefick wrote: install.packages(file.choose(), repos=NULL) thought this would work, but it didn't the package is the sowas package - this doesn't seem to be a CRAN package, and it can be found at : http://tocsy.agnld.uni-potsdam.de/wavelets/ On Wed, Jun 25, 2008 at 8:25 AM, stephen sefick [EMAIL PROTECTED] wrote: I can't figure this one out- I am the administrator, The file that I want to install is a .tar.gz which is located on my desktop. How do I get it into my packages directory- through the GUI or through brute force? thanks stephen -- Let's not spend our time and resources thinking about things that are so little or so large that all they really do for us is puff us up and make us feel like gods. We are mammals, and have not exhausted the annoying little problems of being mammals. -K. Mullis -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
[R] Suppressing output (e.g. from cat)
Is it possible to temporarily suspend output? I am using a function that gives lots of output using cat, that is not very informative. Is it possible to turn output off, run the function, then turn output back on again? I've looked at ?options and done various RSiteSearch()s but couldn't find a way to do this. Many thanks, Richard. -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
Re: [R] Suppressing output (e.g. from cat)
Wacek, many thanks! I'm wondering however whether this will be problematic on Windows (I have no windows box to hand to check this, but am creating a package that I would like to be cross-platform)? Richard. Wacek Kusnierczyk wrote: Richard Pearson wrote: Is it possible to temporarily suspend output? I am using a function that gives lots of output using cat, that is not very informative. Is it possible to turn output off, run the function, then turn output back on again? I've looked at ?options and done various RSiteSearch()s but couldn't find a way to do this. sink(/dev/null) ?sink vQ __ 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. -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
Re: [R] Suppressing output (e.g. from cat)
Many thanks Brian and Hadley, the quiet function works well for me. Maybe a
candidate for utils?
Best wishes
Richard.
hadley wickham wrote:
Or:
tc - textConnection(NULL, w)
sink(tc)
...
sink()
close(tc)
That is a lot more expensive and subject to
o Use of textConnection(NULL, mode=w) could segfault.
(NEWS for 2.7.1). Output textConnections are convenient, but have quite a
lot of overhead since they need to keep the character vector current.
That's true and I hadn't considered the speed issue. It would be nice
to have an analogue to capture.output though. Maybe:
quiet - function(x) {
sink(tempfile())
on.exit(sink())
invisible(force(x))
}
?
Hadley
--
Richard D. Pearson [EMAIL PROTECTED]
School of Computer Science,http://www.cs.man.ac.uk/~pearsonr
University of Manchester, Tel: +44 161 275 6178
Oxford Road, Mob: +44 7971 221181
Manchester M13 9PL, UK.Fax: +44 161 275 6204
__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Extracting row.names
As a further aside, names is also not the best choice for a variable name for the same reason. Richard. Erik Iverson wrote: row.names is a function that takes a data.frame as an argument. So how about row.names(data) ? As an aside, 'data' is not the best choice for a variable name in R, since there is a function called 'data' that will get overridden if you do this ... Patrick Richardson wrote: List, I'm trying to extract the row names of a table I have read into R. data - read.table(mesodata.txt, header=TRUE, row.names=1) When I try to extract them using, names - data$row.names I get, names NULL I've tried changing to a matrix, data frame, etc. and still get NULL. I've checked ?row.names as well as help on extracting part of an object, etc. and unless I'm missing something obvious (likely), I can't figure out how to extract them. BACKGROUND I want to extract the row names (which are basically gene id's) as well as some other columns (which I can do successfully) and cbind them into another data frame (which I can also do successfully). I just can't get the row names extracted (Assigned) to an seperate object. Any suggestions would be appreciated. Many Thanks, Patrick sessionInfo() R version 2.7.0 (2008-04-22) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] stats graphics grDevices utils datasets methods base __ 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. -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
Re: [R] which question
I didn't get any attached data, but my suspicion here is that you have somehow got RefSeq IDs in column 8 of human, as well as the gene symbols. Did you read this data in from a text file? Eleni Christodoulou wrote: An example is: symbol=human[which(human[,3] %in% genes.sam.names),8] The data* human* and *genes.sam.names* are attached. The result of the above command is: symbol [1] CCL18 MARCO SYT13 [4] FOXC1 CDH3 [7] CA12 CELSR1 NM_018440 [10] MICROTUBULE-ASSOCIATED NM_015529 ESR1 [13] PHGDH GABRP LGMN [16] MMP9 BMP7 KLF5 [19] RIPK2 GATA3 NM_032023 [22] TRIM2 CCND1 MMP12 [25] LDHB AF493978 SOD2 [28] SOD2 SOD2 NME5 [31] STC2 RBP1 ROPN1 [34] RDH10 KRTHB1 SLPI [37] BBOX1 FOXA1 NM_005669 [40] MCCC2 CHI3L1 GSTM3 [43] LPIN1 DSC2 FADS2 [46] ELF5 CYP1B1 LMO4 [49] AL035297 NM_152398 AB018342 [52] PIK3R1 NFKBIE MLZE [55] NFIB NM_052997 NM_006023 [58] CPB1 CXCL13 CBR3 [61] NM_017527 FABP7 DACH [64] IFI27 ACOX2 CXCL11 [67] UGP2 CLDN4 M12740 [70] IGKC IGKC CLECSF12 [73] AY069977 HOXB2 SOX11 [76]NM_017422 TLR2 [79] CKS1B BC017946 APOBEC3B [82]HLA-DRB1 HLA-DQB1 [85]CCL13 C4orf7 [88]NM_173552 21345 Levels: (2 (32 (55.11 (AIB-1) (ALU (CAK1) (CAP4) (CASPASE ... ZYX As you can see, apart from gene symbols, which is the required thing, RefSeq ID sare also retrieved... Thanks a lot, Eleni On Fri, Jun 6, 2008 at 1:23 PM, Dieter Menne [EMAIL PROTECTED] wrote: Eleni Christodoulou elenichri at gmail.com writes: I was trying to select a column of a data frame using the *which* command. I was actually selecting the rows of the data frame using *which, *and then displayed a certain column of it. The command that I was using is: sequence=*mydata*[*which*(human[,3] %in% genes.sam.names),*9*] Please provide a running example. The *mydata* are difficult to read. Dieter __ 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. [[alternative HTML version 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. -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
Re: [R] Remove an object by the reference
How about rm(list=x)?
Richard.
Shubha Vishwanath Karanth wrote:
Hi R,
A simple question, but don't know the answer...
x=a
a=5
I need to remove the object a by using only x. something like
rm(somefunction(x))...Is this possible?
Shubha Karanth | Amba Research
Ph +91 80 3980 8031 | Mob +91 94 4886 4510
Bangalore * Colombo * London * New York * San José * Singapore *
www.ambaresearch.com
This e-mail may contain confidential and/or privileged i...{{dropped:13}}
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Richard D. Pearson [EMAIL PROTECTED]
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Re: [R] generic question - Genomics with R
I'd also suggest you check out http://www.bioconductor.org - Bioconductor is an open source and open development software project for the analysis and comprehension of genomic data Richard. Liviu Andronic wrote: Hello, On 4/29/08, [Ricardo Rodriguez] Your XEN ICT Team [EMAIL PROTECTED] wrote: I am trying to make my mind about the use of R for Computational and Statistical Approaches to Genomics. [..] Please, could you help me to go in the right direction? I am not sure what pointers you are looking for, but checking the CRAN Task Views [1] may be a starting point. Liviu [1] http://cran.r-project.org/web/views/index.html __ 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. -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
Re: [R] deleting variables
?rm Richard Ralf Goertz wrote: How can I automatically exclude one variable from being saved in the workspace when I quit an R session? The problem is I don't know how to erase a variable once it has been created. Background: I open a connection called con to a database server in my ~/.Rprofile. Obviously, the connection expires when quitting the R session. Unfortunately, the workspace is loaded after ~/.Rprofile is run. So con get overwritten by the old workspace. I thought of using .First() or .Last() but as these are functions I don't know how to modify global variables. Ralf __ 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. -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
Re: [R] Set of well distinguishable line types?
I've used the following to get a few different line types. However, I'd be interested to hear from someone with expertise in creating line types that are maximally distinguishable by human eyes. ltys = c(22, 44, 13, 1343, 73, 2262, 12223242, F282, F4448444, 224282F2, F1) Best wishes Richard. Jim Lemon wrote: Werner Wernersen wrote: Hi, I am plotting several lines into one plot and would like them to be distinguishable in print later on as well. Thus, my question is: Is there a larger set of such line types available like the sets available for colors? Maybe somebody has already put in the work to define some additional good looking and distinguishable line types. Hi Werner, If you look at lty, there is an option for defining broken line types by strings of up to 8 hexadecimal digits, e.g. abline(h=1,lty=28f8) gives a line like the centerline used in mechanical drawing. Jim __ 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. -- Richard D. Pearson [EMAIL PROTECTED] School of Computer Science,http://www.cs.man.ac.uk/~pearsonr University of Manchester, Tel: +44 161 275 6178 Oxford Road, Mob: +44 7971 221181 Manchester M13 9PL, UK.Fax: +44 161 275 6204 __ 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.
Re: [R] Equivalent of TensorRank
length(dim())?
Amit Soni wrote:
Hi,
In Mathematica, if we have a 3X3 matrix A, we can get its dimensions by:
Dimensions[A] = {3,3}
TensorRank[A] = 2
In R, we have dim() for Dimensions[]. Is there any direct function similar
to TensorRank in R?
Thank you
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Re: [R] ROC analysis
Eleni Does the fpr.stop argument do what you want? This is described in ?performance under the details of the auc measure. Try, e.g. perform=performance(pred,measure=auc,fpr.stop=0.5) Richard. Eleni Christodoulou wrote: Hello list, I am trying to perform ROC analysis and count the AUC in order to validate my results. I use package ROCR. I would like to count the AUC not under the cutoff found by performance but to use another cutoff that I calculate. How could I change the following command in order to get what I want? perform=performance(pred,measure=auc,x.measure=cutoff), where pred is a prediction object. Thank you very much, Eleni [[alternative HTML version 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. __ 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.
Re: [R] levels() function for a vector
Karen levels returns the levels attribute of a variable, and a vector has no such attribute. This is usually used with a factor, e.g. temp - c(3, 5, 5, NA) levels(factor(temp)) [1] 3 5 Best wishes Richard Chang Liu wrote: Hello: I'm trying to use levels function, but I don't know why it's returning NULL. For example: temp[1] 3 5 5 NA levels(temp)NULL Also, I've tried: list(temp)[[1]][1] 3 5 5 NA levels(list(temp))NULL Is there a specific requirement on the parameter? Karen _ [[alternative HTML version 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. __ 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.
Re: [R] how to create ROC curve for 2 dimensional classifiers
I'm not aware of any packages for doing such plots. Conceptually, presumably a ROC curve for a 2d classifier would be a 3d chart, with x-axis being FPR for 1st classifier, z-axis being FPR for 2nd classifier and y-axis being TPR. You would get a ROC surface rather than a ROC curve. Does that make sense? Regards Richard. Waverley wrote: Hi, I understand for 1 d classifiers, you can use ROCR package. Is there a package you can plot ROC curve for 2d classifiers? One of my colleagues asked me about this. I have been quite puzzled, conceptually, how you can do the ROC curve for 2d classifiers. Can someone share his/her knowledge or experience? Thanks in advance. __ 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.
Re: [R] How to make t.test handle NA and essentially constant values ?
Do you mean to deal with the situation where you're doing many t-tests
in a loop? If so there was a post very recently on this list about this:
https://stat.ethz.ch/pipermail/r-help/2008-February/153254.html
Richard.
Ng Stanley wrote:
Thanks. Someone please help to make t.test go through all the data and not
to be disrupted by the two problems.
On 2/12/08, Petr PIKAL [EMAIL PROTECTED] wrote:
Hi
[EMAIL PROTECTED] napsal dne 12.02.2008 09:09:23:
Hi,
First problem:
test - matrix(c(1,1,2,1), 2,2)
apply(test, 1, function(x) { t.test(x) $p.value })
Error in t.test.default(x) : data are essentially constant
make your data not constant
Second problem:
test - matrix(c(1,0,NA,1), 2,2)
apply(test, 1, function(x) { t.test(x) $p.value })
Error in t.test.default(x) : not enough 'x' observations
increase number of observations
How to make t-test ignores this errors ?
Well, the procedure is complaining that you do not give it correct data.
You shall be gratefull for a great software which prevent you from making
silly things as try to compute t.test when data have zero variantion or
number of observations is 1.
Regards
Petr
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