similar to: Simple Question?

Dear list, I wish to plot chromatin precipitation data: I would like to have a rectangles (x:end-start, y:peak) but I do not have an idea how to define x (in terms of qplot syntax) and to choose the correct geom. mydata is a subset of a larger file. > mydata chrom start end peak 1 chr11 5291000 5291926 8 2 chr11 10988025 10988526 7 3 chr11 11767950 11768676 8 4

Need way to resize an existing graphics window. This should be applicable across platforms (as part of a package). Context: function1() draws main plot (I'm using grid), function2() adds smaller plot above main plot, but this one can sometimes overflow the original graphics window area. Thanks, Sigal

Hi Jim I am trying to prepare a bed file to load as accustom track on the UCSC genome browser. I have a data frame that looks like the one below. > x V1 V2 V3 1 chr1 11255 55 2 chr1 11320 29 3 chr1 11400 45 4 chr2 21680 35 5 chr2 21750 84 6 chr2 21820 29 7 chr2 31890 46 8 chr3 32100 29 9 chr3 52380 29 10 chr3 66450 46 I would like to insert the following 4 lines at the beginning:

Hello all, I have written a for loop to act on a dataframe with close to 3million rows and 6 columns and I would like to pass it to apply() to speed the process up (I let the loop run for 2 days before stopping it and it had only gone through 200,000 rows) but I am really struggling to find a way to pass the arguments. Below are the loop and the head of the dataframe I am working on. Any hints

Hello, I am a total beginner with ?R? and found a package ?venn? to create a venn diagram. The problem is, I cannot create the vectors required for the diagram. The manual say: "R> venn(accession, libname, main = "All samples") where accession was a vector containing the codes identifying the RNA sequences, and libname was a vector containing the codes identifying the

I've got two tables.... first one(table1): ID chrom start end Ex1 2 152 180 Ex2 10 2000 2220 Ex3 15 3000 4000 second one ( table2): chrom location name 2 160 Alv 2 190 GNN 2 100

Hi, I'm trying to match peaks between chromatographic runs. I'm able to match peaks when they are chromatographed with the same method, but not when there are different methods are used and spectra comes in to play. While searching I found the ALS package which should be usefull for my application, but I couldn't figure it out. I made some dummy chroms with R, which mimic my actual

Dear Oscar,   Thanks for your help.It's so nice of you to explain this package to me.   Best Regards,   James LAN 发件人： Oscar Rueda [via R] <ml-node+s789695n4431468h14@n4.nabble.com> 收件人： monkeylan <lanjinchi@yahoo.com.cn> 发送日期： 2012年2月29日, 星期三, 下午 9:21 主题: Re: Bayesian Hidden Markov Models Dear James, The distances are normalized between zero and 1, so in your case all of

Dear R users, I need to merge two data frames based on both equal and unequal comparisons. The "sqldf" package used to work well , but today, I cannot resolve the following error by reinstallation of the sqldf package. Can anyone suggest a different way to perform this kind of merge function? Thank you, Ding > DMRlog2pbde47DMS <- sqldf("select * from DMR_log2pbde47 as a

Dear all, I have data.frame object in R. I want to export it in tab-delimited file with several lines of header initiated with comment sign (#). I do not know how to do that in R. Could you please give helps on this problem? Thanks in advance. Best, Jian-Feng, ################################################################## The lines I want to write in the header lines look like, with words

Hi, i have two files (file1.txt and file2.txt) which i would like to merge, based on certain criteria, i.e. it combines data based on matching geneID and exons. i have used the merge option, but it does not give me the desired outcome. merged.txt shows the result i would like. *File1. txt* ** AffyProbe ProbeType Flag GeneSymbol GeneID Exons Chrom Strand Affytart AffyEnd 1

I have a function that does some plotting. I then add lines to the plot. If executed one line at a time, there is not a problem. If I execute the function, though, I get: Error in ans[[1]] : subscript out of bounds This always occurs after the second lines command, and doesn't happen with all of my data points (some do not have errors). Any ideas? Thanks, Sean

Hello, I am using Mechanize to post a form to a website. When I do this by hand in my browser the response takes about 35s to come back (it''s a long page full of tables and graphics). When I do this with Mechanize, the server starts to respond and then appears to hang. The obvious conclusion is that my code is wrong but I am reasonably sure that I haven''t altered it

New user here. My goal is pull daily averages from a long dataset. I've been working with some code I got from this list from https://stat.ethz.ch/pipermail/r-help/2009-March/191302.html The code how I have been using it is as follows: library(zoo) library(chron) DB<-read.table("/Users/me/Desktop/R/data.csv", sep=",", header=TRUE, as.is =TRUE) z<-zoo(LTER6$temp,

Hello R Developers I am using DNACopy package http://bioconductor.org/packages/1.9/bioc/html/DNAcopy.html I am not able to figure out how to (if at all possible) to modify output format, namely, I am getting the following: "ID" "chrom" "loc.start" "loc.end" "num.mark" "seg.mean" Is it a way to get also median and standard deviation?

Hello! First time posting here: Here is my code: x <- c(1:22) finaloutput=cidrm=NULL finaldiversityoutput=diversitym=NULL diversityinfo=read.table("Diversity_info.txt", header=T, sep="\t", row.names=NULL) attach(diversityinfo) diversitynr=nrow(diversityinfo) diversitytemp <- matrix(0,nrow=diversitynr,ncol=1) for(j in 1:length(x)) {

Hi, I have a run of 5 graphs that I want to place them under the same page. Everything works fine to place them in a pdf file , or eps file, but when it comes to have a high quality of 300 dpi these graphs are not good. For example I open the eps file with Adobe Illustrator (AI) and it shows that it is a 72dpi graph. If I start with a 72dpi graph AI cannot improve this to 300 dpi. Q: HOW CAN A

Dear All, I'm using apply to do some genetic association analysis along a chromosome, with many thousands markers. For each marker the analysis is the same, so I was planning to use apply(chrom, 2, somefunction) In the specific case I do: my.results = apply(chr, 2, function(x){anova(lrm( cpstc.f ~ x + time.cpstc + age + sex + mri))[1,3]}) This is all good and well in theory, but in

Hi all, Please bear with me because I'm not all that familiar with R. I manage a research cluster that's running Red Hat 5.6 (64-bit), and we recently installed version 2.15.0 of R for some users. Here's how we built it: ./configure --prefix=/opt/shared/R/2.15.0 --with-tcltk --with-system-zlib --with-system-bzlib --with-system-pcre --with-lapack --enable-R-shlib When we ran

Hi, I was wondering I'm going about this in the correct way. I need to test if there are coding sequences or exons in hg19 which match a string of 100bp "D" i.e. [A,G or T]. However I'm getting a strange result. I get a hit on chr7, using the 100bp search however when I search with 60bp sequence of "D" I don't get any hits. library("BSgenome")