similar to: bug in seq_along

Hi, Is there a mean to automatically choose one version of the 'rbind' function ? By default, R chose the 'rbind' from {base}, i would lke to use the one from {IRanges}... Is it possible to set that using 'par' ? > ?rbind Help on topic 'rbind' was found in the following packages: Package Library IRanges

Hi, when running the following on a fresh R, library("IRanges") annotation showMethods("annotation") Biobase:::annotation showMethods("annotation") I get (see the "^^^^^" marked output at the bottom): > library("IRanges") Carico il pacchetto richiesto: 'IRanges' The following object(s) are masked from package:base :

Hi How to access the values in the output that is an object of S4 type. I tried to access using subset ( [ ] ) but it is not allowed. Any clue?? Thanks -- Fahim #My code is as follows: require(IRanges); query <- IRanges(c(1, 4, 9), c(5, 7, 10)) subject <- IRanges(c(2, 2, 10), c(2, 3, 12)) findOverlaps(query, subject) Output of find overlap function is: ------------------ 1>

Hi I'm missing something here but I cannot figure out what. What I can see is that the same code works when I load it via source(...) yet fails when I execute it after loading the package I have built (which includes the code. Below is a transcript of my R session. First I load the code from a file, using source(). Then I execute it fine. Then I remove the function object, I load the

Thank you Michael Dewey. Can you please send me the email id for Bioconductor. regards Pijush On Fri, Dec 29, 2017 at 5:20 PM, Michael Dewey <lists at dewey.myzen.co.uk> wrote: > Dear Pijush > > You might do better to ask on the Bioconductor list as IRanges does not > seem to be on CRAN so I deduce it is a Bioconductor package too. > > Michael > > > On

Dear Sir, I have been using R for a long time. But recently I have faced a problem when installing the Bioconductor package named "methyAnalysis". Firstly it was require to update my older R (R version 3.4.3 (2017-11-30)) in to newer version. That time I have also updated the RStudio software. After that when I have tried to install the package named "methyAnalysis". It

Dear Pijush You might do better to ask on the Bioconductor list as IRanges does not seem to be on CRAN so I deduce it is a Bioconductor package too. Michael On 29/12/2017 07:29, Pijush Das wrote: > Dear Sir, > > > > > I have been using R for a long time. But recently I have faced a problem > when installing the Bioconductor package named "methyAnalysis".

R CMD build fails with recent R-devel because it is looking for texi2dvi in /usr/local/bin, but on this system, MacTex has installed it in /usr/bin. $ R CMD build IRanges * checking for file 'IRanges/DESCRIPTION' ... OK * preparing 'IRanges': * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes * creating vignettes ... ERROR

Hi, S4 method dispatch can be very slow. Would it be reasonable to cache the most recent dispatch, anticipating the next invocation will be on the same type? This would be very helpful in loops. fun0 <- function(x) sapply(x, paste, collapse="+") fun1 <- function(x) { paste <- selectMethod(paste, class(x[[1]])) sapply(x, paste,

R experts, Hello, I am trying to sample a vector 1:40 without replacement such that no element in the new vector is within 7 units of either of its immediate neighbors. This is part of a larger program I am working on. The following code works well about 65 % of the time (14/40). The problem I encounter happens when the last element remaining to be sampled from the vector STRATA is within 7

I have a few simple questions about the usage of PROTECT, more specifically how careful one needs to be. Simple yes/no answers are fine. Most of the uses I have seen do protection when memory is allocated. But what if one just want to assign a value of another function to a variable. Say eg. that foo is a function that returns a SEXP. Would the following code be fine? SEXP bar;

Dear All, I am trying to finding overlapping regions in two diff datasets for that I am using IRanges. But I am getting an error in the process of doing the overlap. Advance thanks df3.rl<-RangedData(IRanges(start=df3$V3,width=1), + space=df3$start) Error in .normargSEW0(start, "start") : 'start' must be a numeric vector (or NULL) Kumar [[alternative HTML version

Hi Martin, On 11/29/2017 10:46 PM, Martin Morgan wrote: > On 11/29/2017 04:15 PM, T?th D?nes wrote: >> Hi, >> >> A benchmarking study with an additional (data.table-based) solution. > > I don't think speed is the right benchmark (I do agree that correctness > is!). Well, agree, and sorry for the wording. It was really just an exercise and not a full

On 11/29/2017 04:15 PM, T?th D?nes wrote: > Hi, > > A benchmarking study with an additional (data.table-based) solution. I don't think speed is the right benchmark (I do agree that correctness is!). For the R-help list, maybe something about least specialized R knowledge required would be appropriate? I'd say there were some 'hard' solutions -- Michael (deep

Based on some testing it seems to me that if I have a package with a dataset in /data a Sweave vignette in inst/doc (but no associated pdf file) the vignette loads the data in /data through data(dataset) and I do a R CMD build R will try to build the pdf version of the vignette, but will be unable to find the dataset in data because the package is not yet installed. However, if I do

Hi, A benchmarking study with an additional (data.table-based) solution. Enjoy! ;) Cheers, Denes -------------------------- ## packages ########################## library(dplyr) library(data.table) library(IRanges) library(microbenchmark) ## prepare example dataset ########### ## use Bert's example, with 2000 stations instead of 2 d_df <- data.frame( station =

Hi, This is a follow up to: https://stat.ethz.ch/pipermail/r-devel/2010-July/057921.html The Bioconductor daily builds have been reporting a lot of strange things lately on Windows using R-2.12. This started 2 or 3 months ago and things are not getting better with recent R-2.12. Here is a sample from today's build results. We use Windows Server 2003 R2 for the 32-bit builds, Windows

I have a confusing error from R CMD check that I don't get when running the example manually by hand. In the \examples section of an Rd file, I create a GRanges object, then I call a function with the GRanges object, whose first 2 lines are require(GenomicRanges) annoDF <- as.data.frame(anno) # anno is the GRanges object. and that second line gives: Error in

I've started to implement checks for package versions on dependencies in install.packages(). However, this is revealing a number of problems/misconceptions. (A) We do not check versions when loading namespaces, ahd the namespace registry does not contain version information. So that for example (rtracklayer) Depends: R (>= 2.7.0), Biobase, methods, RCurl Imports: XML (>=

Hi, Has anyone know about how to get the correct plot? I have use this R script (as below), so I expect the plot is based on x axis, but the result was opposite. Any suggestion will be great. library(IRanges) data <-read.table(file="~/q20snpref/illusmp454merbed",sep="\t",header=F) colnames(data)<-c("Scaffold","sca_position","coverage")