search for: iranges

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 /us3/gcg18/martial/local/R_lib base /usr/local/lib64/R/library Choose one 1: External D...

I have a question about some strange results I get when using lmer to build a logistic mixed effects model. I have a data set of about 30k points, and I'm trying to do backwards selection to reduce the number of fixed effects in my model. I've got 3 crossed random effects and about 20 or so fixed effects. At a certain point, I get a model (m17) where the fixed effects are like this

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...

...;. 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 shows some error given below. No methods found in package ?IRanges? for requests: ?%in%?, ?elementLengths?, ?elementMetadata?, ?ifelse?, ?queryHits?, ?Rle?, ?subjectHits?, ?t? when loading ?bumphunter? Error: package or namespace load failed for ?methyAnalysis?: objects ?.__T__split:base?, ?split? are not exported by 'namespace:IRanges' In addition: Warni...

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 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 >&g...

Dear All, I am trying to define a loop for a m*n matrix, where i=1:n and j=1:m. Unlike the usual for loop, i should go in the following way: For j=1, i=1,2,3,....n For j=2, i=n,n-1,n-2,......,1 For j=3, i=1,2,3,.....n etc. which means i should go in either increasing or decreasing order alternatively. Can anyone please help me in doing this? Thanks, Cassie [[alternative HTML version

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> findOverlaps(query, tree) An object of class "RangesMatching" Slot "matchMatrix": query...

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 [...] Warning in sub(object$syntax$docexpr, val, chunk[pos[1L]]) : argum...

...;, "flag", "rname", "strand", "pos", "qwidth", "mapq", "cigar", "mrnm", "mpos", "isize", "seq"), tag=c("NM"), removeN=TRUE) { which <- RangesList(chr = IRanges(start,end)) names(which) <- chr param <- ScanBamParam(which = which, what = what, tag=tag) bam <- scanBam(bamfile, param=param) lst <- lapply(names(bam[[1]]), function(elt) {do.call(c, unname(lapply (bam, "[[", elt)))}) names(lst) &lt...

Hello, Suppose in the following code, PROTECT(sr = R_tryEval( .... )) sr is a RAWSXP vector. I wish to return another RAWSXP starting at position 13 onwards (base=0). I could create another RAWSXP of the correct length and then memcpy the required bytes and length to this new one. However is there a more efficient method? Regards Saptarshi Guha

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 "...

...expr min lq median uq max neval ## fun0(lst) 21.093180 21.27616 21.453174 21.833686 24.758791 10 ## fun1(lst) 4.517808 4.53067 4.582641 4.682235 5.121856 10 Dispatch seems to be especially slow when packages are involved, e.g., with the Bioconductor IRanges package (http://bioconductor.org/packages/release/bioc/html/IRanges.html) removeGeneric("paste") library(IRanges) showMethods(paste) ## Function: paste (package BiocGenerics) ## ...="ANY" ## ...="Rle" selectMethod(paste, "ANY") ## Met...

...in as.data.frame.default(anno) : cannot coerce class 'structure("GRanges", package = "GenomicRanges")' into a data.frame Calls: annoGR2DF ... annoGR2DF -> .local -> as.data.frame -> as.data.frame.default I have GenomicRanges listed in my Imports: field, and IRanges in the Suggests: of the DESCRIPTION file (it's require()d elsewhere). I'm trying to avoid putting packages in Depends: , so my package loads fast. Any tips of what I'm not understanding properly ? Thanks. -------------------------------------- Dario Strbenac Research Assistant Cancer...

...unter happens when the last element remaining to be sampled from the vector STRATA is within 7 digits +- of the last element in the vector s1, at which point an infinite loop occurs. At least that's what I think is happening. Any help would be greatly appreciated. Thank you, Mike require(IRanges) STRATA <- 1:40 s1 <- sample(STRATA, 1) for (i in seq(from = 1, to = 39, by = 1)){ repeat{ tmp <- sample(STRATA, 1) if (!any(s1 == tmp) & !any(as.vector(IRanges(s1[length(s1)]-7, s1[length(s1)]+7)) %in% tmp)) break } s1 <- c(s1,tmp) } s1

...on. 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 understanding of Bioconductor and IRanges), Toth (deep understanding of data.table), Jim (at least for me moderate understanding of dplyr,especially the .$ notation; a simpler dplyr answer might have moved this response out of the 'difficult' category, especially given the familiarity of the OP with dplyr). I'd vote for Bi...

Hi: I have a two large files (over 300K lines). file 1: Name X UK 199 UK 230 UK 139 ...... UAE 194 UAE 94 File 2: Name X Y UK 140 180 UK 195 240 UK 304 340 .... I want to select X of File 1 and search if it falls in range of X and Y of File 2 and Print only those lines of File 1 that are in range of File 2 X and Y How can it be done it

...t;subject"]] SubjectPosition Subject Pattern Count Probability 1 2 T A 1 1 2 3 T A 1 1 This could be improved with accessors for end users. Also, instead of being a data.frame, this would be better stored as IRanges with associated metadata columns, accessible with mcols, so that methods like reduce could easily be used to look for contiguous blocks of differences. Is there a reason why the show method for the summary only shows mismatches, even if there are indels contained in it? This seems arbitrary and al...

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 deleted...

...fortunate, as the present example also illustrates. Regards, Denes > > 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 understanding of Bioconductor and IRanges), Toth (deep > understanding of data.table), Jim (at least for me moderate > understanding of dplyr,especially the .$ notation; a simpler dplyr > answer might have moved this response out of the 'difficult' category, > especially given the familiarity of the OP with dplyr)....

Using the IRanges package from Bioconductor and somewhat recent R-2.9.1. ov = IRanges(1:3, 4:6) length(ov) # 3 seq(along = ov) # 1 2 3 as wanted seq_along(ov) # 1! I had expected that the last line would yield 1:3. My guess is that somehow seq_along don't utilize that ov is an S4 class with a length method...