[R] Pathview xml issue

Hi, I'm using GAGE/pathview to analyze my RNA-seq and phospho-protein data. The following error occurs after this command line below: >pv.out.list <- sapply(path.ids2[1:3], function(pid) pathview( gene.data = cnts.d, pathway.id = pid, gene.idtype="SYMBOL",kegg.native = F, same.layer = T, spec

Re: [R] Fwd: only plot borders of a region in a scatter plot

contour to be 90 degree. Another problem for the contour() is that the contour line doesn't close at where the value of neighbouring grid cell is NA. See the right side of the two contour lines (attachment). Do you know how I can get what I want? Thanks a lot :P Cheers, Zun Yin On Thu,

[R] User defined function within a formula

Hello, I have a question about the formula and the user defined function: I can do following: ###Case 1: > clotting <- data.frame( + u = c(5,10,15,20,30,40,60,80,100), + lot1 = c(118,58,42,35,27,25,21,19,18), + lot2 = c(69,35,26,21,18,16,13,12,12)) > g1=glm(lot1 ~ log(u) + poly(u,1), d

Re: [R] User defined function within a formula

alls to be used for > prediction: >> attr(g2$terms, "variables") >list(lot1, log(u), xpoly(u, 1)) > > attr(g2$terms, "predvars") > list(lot1, log(u), xpoly(u, 1, coefs = list(alpha = 40, norm2 = c(1, > 9, 8850 > > > >

Re: [R] User defined function within a formula

like makepredictcall.scale() and scale() for an >> example: >> scale has optional arguments 'center' and 'scale' that it returns as >> attributes >> and makepredictcall.scale adds those to the call to scale that it is >> given. >> Thus when you pre

[R] solve heywood case within R

Hello. Sorry to bother you, but this is the email address I got from r-help... I am wondering if R has some similar command like SAS to solve heywood cases. If there some related functions/program, would you give me some help on that? Thank you very much. With regards, Yin Chang

[R] s4 class documentation in R

uggestions for me? Thanks Regards Tengfei -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name English Blog: www.tengfei.name/en Chinese Blog: www.tengfei.name/ch [[alternative HTML versi

[R] how to manipulate object in specific environment?

tion myfun(), when I run myfun(), this retrieve all the objects in my environment automatically and print their mode or class one by one. Thanks Regards Tengfei -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name En

Re: [R] how to manipulate object in specific environment?

Hi Henrique, Thank you so much, that's exactly what I want! Thanks again Tengfei On Thu, Apr 8, 2010 at 3:28 PM, Henrique Dallazuanna wrote: > See ?eapply > > On Thu, Apr 8, 2010 at 5:01 PM, Tengfei Yin wrote: > > Hi > > > > I want to simplify my problem

Re: [R] R GUI

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. > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274

Re: [R] Select single column, preserve name?

vious way to subset just one column and retain > its name? > > Thanks, > Duncan > > __ > R-help@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-projec

Re: [R] A question about plot.mcmc

> 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/

Re: [R] A question about plot.mcmc

Hi David, Thank you so much, that's just what I want!! Best Tengfei On Wed, Apr 21, 2010 at 2:24 PM, David Winsemius wrote: > > On Apr 21, 2010, at 3:21 PM, Tengfei Yin wrote: > > Hi >> >> I have mone quick question I am not quite familiar with, for generic >&

[R] R for Ubuntu 10.04?

t know if there is going to be a R release that will support this newly released Ubuntu? Thanks Best wishes Tengfei -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[alternative HTML

Re: [R] R for Ubuntu 10.04?

w, I could upgrade my R to 2.11 and then upgrade my system to Lucid. Thanks again for your suggestions! Best Tengfei On Tue, Apr 27, 2010 at 11:20 AM, Jeff Newmiller wrote: > Tengfei Yin wrote: > >> Hi dear all >> >> I am currently using Ubuntu 9.10 (karmic) and R 2.10,

Re: [R] by funtion

gt; > __ > 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] by funtion

-by(test[,2:5], feature, mean) > > > I found aa is "by" function. > > > > class(aa) > > > [1] "by" > > > > > > how can I transfer aa to a data frame? > > > > > > thanks > > > YU > &g

Re: [R] by funtion

> name c5 c6 > > 1 BB 98 7 > > 2 AA 87 6 > > 3 DD 54 3 > > > > now I want to get interaction for df and df1 in terms of name. this is > > name c1 c2 c3c4 c5 c6 > > AA 23 54 0.999 0.78 87 6 > > B

Re: [R] How to extract data table

elp mailing list archive at Nabble.com. > > __ > 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] Is there an equivalent of type="where" in predict.rpart, similiar to tree?

In package tree, users can use predict(model,data,type="where") to find out which terminal node the observation belongs to. I can't seem to find a similar function in package rpart. Is there any way to find out the same information using rpart? Thanks! Yin Luo

Re: [R] Manhattan Plot

://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. > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274

[R] prediction.strength in r package fpc

Hi i am using prediction.strength with k-medoids algorithms. There are simple examples like prediction.strength(iriss,2,3,M=3,method="pam") I wrote my code like prediction.strength(data,2,6,M=10,clustermethod=pamkCBI,DIST,krange=2:6,diss=TRUE,usepam=TRUE) because i am using the dissimilarit

[R] How to deal with multiple class ROC analysis in R (pROC package)?

Here is the question link: http://stackoverflow.com/questions/20507108/how-to-deal-with-multiple-class-roc-analysis-in-r-proc-package Thanks! -- *Yin Zhao <http://www.linkedin.com/in/zhaoyin>* *My Blogger <http://ameenzhao.blogspot.com/>* [[alternative HTML ver

Re: [R] R crashes with large vectors

> 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. > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames,

[R] 测试

²âÊÔ -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r

[R] 测试3

²âÊÔ3 -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 Homepage: www.tengfei.name [[alternative HTML version deleted]] __ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r

[R] 测试4测试4测试4测试4

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Re: [R] 测试3

Sorry! I apologize for my mistake! 2010/8/15 Tengfei Yin > ²âÊÔ3 > > -- > Tengfei Yin > MCDB PhD student > 1620 Howe Hall, 2274, > Iowa State University > Ames, IA,50011-2274 > Homepage: www.tengfei.name > > > -- Tengfei Yin MCDB PhD stud

[R] Sorry, I have changed the Chinese R help mailing list name to avoid similarity problem.

the Chinese mailing list name to, without prefix 'r-', or any other mailing list, below is the new one. h...@r-china.org In order to avoid auto-complete mistake in the future. Sorry to bother you guys Thanks Tengfei -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State

Re: [R] installing a package in linux

-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. > -- Tengfei Yin MCDB Ph

Re: [R] installing a package in linux

mail.com> wrote: > On 05/05/2010 02:44 AM, Tengfei Yin wrote: > >> Hi >> >> R basic packages always works fine in my laptop (also ubuntu), you don't >> need to reinstall anything once you installed the package, did you do that >> in your terminal like >>

[R] reshape cast to a sparse matrix?

there strategies or other packages that that may be useful? Due to memory constraints, it would be best to convert to sparse matrix on the fly rather than build the full matrix and then convert it. Thanks for the help, Yin [[alternative HTML version de

[R] Bezier curve in R?

Hi dear all, I am wondering if there is a function existing in R that did the quadratic bezier curve interpolation? I hope to generate a bezier curve based on three sets of points: two end of the line and a control point. Thanks in advance. Tengfei -- Tengfei Yin MCDB PhD student 1620 Howe

Re: [R] Bezier curve in R?

Hi Prof. Frank Harrell, The bezier function in Hmisc package is exactly what I am looking for. Thanks a lot! Tengfei On Tue, Nov 22, 2011 at 2:55 PM, Frank Harrell wrote: > require(Hmisc) > ?bezier > ?drawPlot > > Frank > > Tengfei Yin wrote > > > > Hi de

Re: [R] Help! I couldn't put multiple qplot on the same page...

ect.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. > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State

[R] ggExtra package installation fails

acks. And I don't really want to write my own hack function(and don't know how yet) to do that, if there is already a nice function for the same purpose~ Thanks~ Tengfei -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA

Re: [R] ggExtra package installation fails

lot2 graphics? thanks a lot. > > baptiste > > > > On 16 January 2012 11:21, Milan Bouchet-Valat wrote: > > Le dimanche 15 janvier 2012 à 15:43 -0600, Tengfei Yin a écrit : > >> Hi dear all, > >> > >> I cannot find ggExtra source code or install

[R] semi-transparency not supported in devel R? "alpha" cannot be specified in qplot()

d here, because if I miss some important system dependencies, why it's still working in R 2.14? Any suggestions or possible solution will be really appreciated. Thanks Tengfei -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa State University Ames, IA,50011-2274 [[alter

Re: [R] Interactive map graphics.

info/r-help> > PLEASE do read the posting guide http://www.R-project.org/** > posting-guide.html <http://www.R-project.org/posting-guide.html> > and provide commented, minimal, self-contained, reproducible code. > -- Tengfei Yin MCDB PhD student 1620 Howe Hall, 2274, Iowa St

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

> Bioconductor mailing list > bioconduc...@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Tengfei Yin MCDB PhD student 1620 Howe H