Re: [R] help needed for HWE.exact in library "genetics"

You could follow the advice given when loading the library (see the code you posted for details) and use the enhanced genetics packages to cross-validate the results (ideally you should get the same answer). The results not weird though. Your working with SNPs and having a homozygote with a freq

Re: [R] Spider Graph

Van Patten, Isaac T wrote: > > Is there an R function to generate a radar or spider graph from a table > - e.g.radar(table(x)) or some such? > And you may find this a useful site to bookmark... http://addictedtor.free.fr/graphiques/ Neil -- View this message in context: http://www.n

Re: [R] Literature analysis

On Fri, Dec 11, 2009 at 2:04 PM, Schwan wrote: > Thanks, but how should I put the citation inside a data frame? > > data.frame(first txt file, second txt file...) > plot (what should I insert here) type="p" > > And how should I load the txt files anyway inside the frame? > Check out the resou

Re: [R] Pros and Cons of R

Installation under Gentoo is straightforward too (emerge dev-lang/R). Updating has never really been a problem. CRAN packages are rebuilt if needed when updating R, and periodically all you need to do is fire up R and use update.packages() to update any packages you've installed. Another pro to

Re: [R] Pros and Cons of R

I feel the discussion about ease of installation on Linux (/*NIX type systems) isn't really relevant to the Pros and Cons of R. The problems encountered by people are often a consequence of their lack of knowledge/understanding of the operating system, and not a deficiency of R itself. Just my t

Re: [R] How to make R running faster

ctu wrote: > > Hi everyone, > I run the R loops on window XP and vista. Both are Intel core 2 Duo > 2.2 GHz with 2 GB ram and XP is significantly faster than vista. Dose > anyone know how speed up R loops in vista? > > Loops are not massively efficient within R. Look into using the appl

Re: [R] problem in installing R packages on linux

man4ish wrote: > > > No i am trying to install BART which is valid name , i have 30-40 times > for other packages still facing the same pblm .How can i rectify > this.Please help me out. > Rather than sending a screenshot of a terminal (and note the posting guidelines with regards to attachm

Re: [R] genotypes simulation

Claire_6700 wrote: > > Hello, > > I am having really hard time finding a good article about simulating > genotypes of cases and controls at a disease locus using R. > > if you guys can point me or guide me where i can find more information, it > will be helpful. > > The popgen() package al

Re: [R] Importing data

Yemi Oyeyemi wrote: > > Hi everyone, please I'm having problem importing data from Stata and > excel. Help me out. > Thanks > > You don't provide... a) the code that you've tried b) the error message that relates to the problem you are having ...without these people have little informat

Re: [R] scrime Package simulatedSNP function

Claire_6700 wrote: > > Hello, > > I need some help with the simulatedSNPs function from scrime package. > > I am trying to simulate some genotype of a case/control disease locus. The > allele frequence are cases/controls > > Sample cases controls > 2000 .5.10 > 1

[R] Package specific dependencies...

Hi, I noticed recently when installing the GDD package for R under GNU/Linux that it required the gd library (http://libgd.org/) for generating graphics. The resolution of this was to simply install the library on my system, and then GDD successfully installed without any complaints. However, th

Re: [R] Package specific dependencies...

On Nov 22, 2007 4:14 PM, Gabor Grothendieck <[EMAIL PROTECTED]> wrote: > The SystemRequirements field on the DESCRIPTION file is used > to document the system requirements. For example, the DESCRIPTION > file for Ryacas (which requires yacas) is shown below. > > Package: Ryacas > Version: 0.2-8 >

Re: [R] editor under MAC system

YIHSU CHEN-3 wrote: > > Dear R-user; > I recently switched from PC to MAC. Is there a compatible editor as > Win-editor with package RWinEdit for MAC? > > I'd recommend using Emacs with ESS (see http://ess.r-project.org/). The advantage of this (beyond the seamless integration) is that its

Re: [R] I need arguments pro-S-PLUS and against SAS...

You might find this article useful Kellie B. Keeling and Robert J. Pavur, A comparative study of the reliability of nine statistical software packages, Computational Statistics & Data Analysis, Volume 51, Issue 8, 1 May 2007, Pages 3811-3831. (http://www.sciencedirect.com/science/article/B6V8

Re: [R] How to draw a plot like this?

Jinsong Zhao wrote: > > Hi there, > > I hope to draw a plot like this: > http://www.sg-chem.net/swizard/Ru-bqdi-spectra.gif > > is it possible to draw it using R? > > thanks for any suggestions. > My intuition would say yes it is possible as R graphics are highly flexible. I'm afraid I don

Re: [R] How to create a chromosome location map by locus ID

Sake wrote: > > Hi, > > I'm trying to make a chromosomal map in R by using the locus. I have a > list of genes and their locus, and I want to visualise that so you can see > if there are multiple genes on a specific place on a chromosome. A example > of what I more or less want is below: > ht

Re: [R] PDF slided (beamer or prosper) to an editable PPT

zubin-2 wrote: > > Hello, I am getting requests to place our PDF slides (output from > beamer) into Microsoft Powerpoint formats (.ppt). What's the best > practice or any recommended software packages (any success with open or > commercial) that we can use to convert PDF slides into an EDIT

Re: [R] Perl-R bridge

ANJAN PURKAYASTHA wrote: > > Hi, > I'm planning to access R from my perl scripts. > The only noteworthy bridge seems to be > Statistics-R-0.03. > Would anyone like to share their experience with this Perl-R bridge? Irrespectiv

Re: [R] Does anyone has this paper in pdf?

aiminy wrote: > > de Jong, S. (1993) SIMPLS: an alternative approach to partial least > squares > regression. Chemometrics and Intelligent Laboratory Systems, 18, 251–263 > > Yes, the publishers do, you can purchase it from http://dx.doi.org/10.1016/0169-7439(93)85002-X Its a shame that no

Re: [R] Does anyone has this paper in pdf?

Rolf Turner-3 wrote: > > > Is this really a violation of copyright? If I have a copy of a > journal I believe > it is within the compass of ``fair practice'' (or some such jargon) > to make a photocopy > of a particular article and give this copy to a colleague or student > for research

Re: [R] How do I get my IT department to "bless" R?

Daniel Viar wrote: > > I currently use R at work "under the radar", but there's a chance I > could loose that access. I'd like to get our company to feel > comfortable with open source and R in particular. Does anyone have > any experience with their company's IT department and management tha

Re: [R] Problems in Recommending R

Adam D. I. Kramer-2 wrote: > > I respectfully disagree. In my repeated experience, I have seen colleagues > in industry and university simply write R off as "too difficult" or "not > worth the effort" based on purely cosmetic grounds, and then at my urging > and after some instruction embrace R

Re: [R] Problems in Recommending R

Barry Rowlingson wrote: > > 2009/2/3 Neil Shephard : > >> Again I'd disagree, perhaps the most widely used suite of software has a >> very simple and clean web-site with few bells and whistles, ditto for one >> of >> the most popular text-editors. I

Re: [R] Problems in Recommending R

hadley wrote: > > Have you ever used the R website? > > To download the latest version for R for windows you have to: > No I don't use windows and install R via the package management system of my chosen distribution (http://www.gentoo.org/). That said I have installed from source in the pa

Re: [R] Problems in Recommending R

hadley wrote: > >> The most useful thing (and quite rightly so) on the front page is the >> link >> the the FAQ which should be the starting point for anyone looking at any >> new >> software, and answers/explains everything thats pertinent! (At least >> thats >> what I read first when I start

Re: [R] Problems in Recommending R

Warren Young wrote: > > Yyeahhh...look how much that sort of stance has helped the cause of > Linux on the desktop. World domination has been a year or two away for > the last 10 years. (Speaking as one who uses Linux every day, and used > it as his main desktop at home for many years befor

Re: [R] Best 64-bit Linux distro for R?

KMSL wrote: > > I'm running R on the current version of Gentoo and had no trouble building > the complete system required. The only problem is that the current > version in portage (stable) is 2.7.2. > > The latest _stable_ version (in terms of Gentoo's testing and release policy, NOT R's)

Re: [R] installing R on Ubuntu

The preceived "difficulty" of installing R under whatever flavour of GNU/Linux in this thread stems from being unfamiliar with the process of the package management of the flavour of GNU/Linux you use (and in part by the various distros not having the most recent version of R in their repositories

Re: [R] installing R on Ubuntu

znmeb wrote: > > On Mon, Feb 9, 2009 at 4:51 AM, Neil Shephard wrote: >> >> There are pro's and con's to each of the GNU/Linux flavours and its >> really a >> matter of deciding which you like/have invested time in learning. >> >> Irrespec

Re: [R] Fwd: Converting R to Sweave (Rnw)

Rainer M Krug-6 wrote: > > Hi > > I am thinking about using Sweave more frequently, especially for > documenting code. But the syntax is slightly awkward for me (<>= > ... @), and I was thinking if there would be a way of importing the > type of code extracted from an Rnw file back into an Rnw

Re: [R] multiple hypothesis testing

Vijaykumar Muley wrote: > > Dear all, > > Myself Vijaykumar Muley working as senior research fellow. By training I > am > a computational biologist with not a strong knowledge of statistics. I > have > done some analysis which is explained as follows, > > I have 10340 (X) profiles of binary v

Re: [R] How to search for packages - wrap up!

Charilaos Skiadas-3 wrote: > > On Feb 5, 2008, at 10:37 AM, Monica Pisica wrote: > > But perhaps I am missing something very obvious? > > I thought the task views were located where they are (linked from the page that lists packages) as they summarise the available packages for the given to

Re: [R] How to search for packages - wrap up!

volunteer to (I presume) the R-core team and enter into dialogue with them. Neil On Feb 6, 2008 12:02 PM, Charilaos Skiadas <[EMAIL PROTECTED]> wrote: > > On Feb 6, 2008, at 6:23 AM, Neil Shephard wrote: > > > Charilaos Skiadas-3 wrote: > >> > >> On Fe

[R] Problems reshaping data with cast()

Hi, I'm trying to cast() some data, but keep on getting the following error... > norm.all.melted.height <- transform(all.melted.height, + norm.height = value / ave(value, SNP, Pool, FUN = max) + ) Warning messages: 1: In FUN(

Re: [R] Problems reshaping data with cast()

On Feb 7, 2008 2:21 PM, hadley wickham <[EMAIL PROTECTED]> wrote: > Hi Neil, > > I think your cast statement is wrong. You have > > cast(norm.all.melted.height, Sample.Name + SNP + Pool ~ value, sum) > > but I think you want > > cast(norm.all.melted.height, Sample.Name + SNP + Pool ~ ., sum) > > i

Re: [R] kinship package: drawing pedigree error

You can also draw pedigrees using the pedtodot() function from the gap package. It does however depend on graphviz (http://www.graphviz.org). An article on drawing pedigrees in R is available in Bioinformatics 22(8):1013-1014 (see http://forums.gentoo.org/viewtopic-t-641204) There _may_ also be

Re: [R] Using R in a university course: dealing with proposal comments

Neil Shephard wrote: > > (Most) of this problem isn't negated when using R. Start a new job and > use the (excellent, extensible, and free) software that you've been using > for years. > Apologies for the double negative, that should have read "(Most) of

Re: [R] Using R in a university course: dealing with proposal comments

Arin Basu-3 wrote: > > Comment 2: > > Finally, on a minor point, why is "R" the statistical software being > used? SPSS is probably more widely available in the workplace – > certainly in areas of social policy etc. " (Prof NB) > > What struck me in the above is the "probably". How probabl

[R] CRAN Taskviews returns 404

The CRAN Taskviews (http://cran.r-project.org/web/packages/Views/) is currently unavailable and returns 404 Object not found! This is possibly due to them now being linked from the side frame and the URL now being http://cran.r-project.org/web/views/ Unfortunately the webmaster link on the 404 p

Re: [R] CRAN Taskviews returns 404

On Feb 18, 2008 2:02 PM, Peter Dalgaard <[EMAIL PROTECTED]> wrote: > > But what gave you the idea that > http://cran.r-project.org/web/packages/Views/ should work? Google seems > not to know it. > Its the target for the link to the TaskViews from http://cran.r-project.org/web/packages/index.html (

[R] Logical statements and subseting data...

Hi, I'm scratching my head as to why I can't use the subset() command to remove one line of data from a data frame. There is just one row (out of 45840) that I'd like to remove and it can be identified using > dim(raw.all.clean) [1] 4584010 > subset(raw.all.clean, Height.1 == 0 & Height.

Re: [R] Logical statements and subseting data...

Thanks Thierry, they do both leave me with what I expected. On Mon, Feb 25, 2008 at 2:28 PM, ONKELINX, Thierry <[EMAIL PROTECTED]> wrote: > The negation of Height.1 == 0 & Height.2 == 0 was incorrect. Use > > subset(raw.all.clean, !(Height.1 == 0 & Height.2 == 0)) I can see clearly how this expr

[R] Errors melt()ing data...

Hi, I'm trying to melt() some data for subsequent cast()ing and am encoutering errors. The overall process requires a couple of casts()s and melt()s. Start Session 1## ## I have the data in a (fully) melted format and can cast it fine... > norm1[1:10,] Pool SNP Sample.Na

Re: [R] Errors melt()ing data...

Hi Hadley, On Thu, Feb 28, 2008 at 1:15 PM, hadley wickham <[EMAIL PROTECTED]> wrote: > > I think the problem is that reshape adds some extra information to the > cast data.frame, but this info is no longer relevant when you've > removed some of the columns. Try as.data.frame to strip off this

Re: [R] Graphic text

Hi Maura, I'm afraid that your message below only came to me, and wasn't copied to R-help. I'm useless at graphics in R, but I'd recommend posting exactly what R-code that your writing, this will show what plotting commands your using and the syntax, and will allow others to provide insightful co

Re: [R] Graphic text

n you have to > present your project then pretty pictures,widgets, and gadgets capture > the attention of the audience. > Maybe R can be interfaced with GL and/or Tcl/Tk. > > Thanks, > Maura > > > > On Fri, Feb 29, 2008 at 10:43 AM, Neil Shephard <[EMAIL PROTECTED