search for: genomicranges

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 as.data.frame.default(anno) : cannot coerce class 'structure("GRanges", package = "GenomicRanges")' into a data.frame Calls: annoGR2DF ... annoGR2DF -> .local...

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

This is about the new note Depends: includes the non-default packages: ‘BiocGenerics’ ‘Biobase’ ‘lattice’ ‘reshape’ ‘GenomicRanges’ ‘Biostrings’ ‘bumphunter’ Adding so many packages to the search path is excessive and importing selectively is preferable. Let us say my package A either uses a class B (by producing an object that has B embedded as a slot) from another package or provides a specific method for a generic define...

Hi all, The function call series genericForPrimitive -> .findBasicFuns -> .findAll happens 4400 times while the GenomicRanges package is loading. Each time .findAll follows a chain of environments to determine that the methods namespace is the only one that holds a variable called .BasicFunsList. This accounts for ~10% of package loading time. I'm sure there is some history to that design, but would it be possible sh...

Hello, I have start and end coordinates from different experiments (DNase hypersensitivity data) and now I would like to combine overlapping intervals. For instance (see my test data below) (2) 30-52 and (3) 49-101 are combined to 30-101. But 49-101 and 70-103 would not be combined because they are on different chromosomes (chr a and chr b). Does anybody have an idea? Thanks Hermann > df

Hi, I want to merge multiple chromosomal regions based on their common intersecting regions. I tried couple of things using while and if loops but did not work out. I would appreciate if anyone could provide me a small piece of code in R to get the intersection of following example: chr1: 100-150 chr1: 79-250 chr1: 100-175 chr1: 300-350 I want the intersection of all four regions as follow:

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

...directly as in > setMethod? > > > On Wed, Jan 21, 2015 at 10:41 AM, Peter Haverty <haverty.peter at gene.com> > wrote: > >> Hi all, >> >> The function call series genericForPrimitive -> .findBasicFuns -> .findAll >> happens 4400 times while the GenomicRanges package is loading. Each time >> .findAll follows a chain of environments to determine that the methods >> namespace is the only one that holds a variable called .BasicFunsList. >> This >> accounts for ~10% of package loading time. I'm sure there is some history >&gt...

...ages: [1] "affy" "affydata" "affyPLM" "affyQCReport" [5] "annaffy" "annotate" "Biobase" "biomaRt" [9] "Biostrings" "DynDoc" "gcrma" "genefilter" [13] "geneplotter" "GenomicRanges" "hgu95av2.db" "limma" [17] "marray" "multtest" "vsn" "xtable" Please wait... Warning in install.packages(pkgs = pkgs, repos = repos, ...) : argument 'lib' is missing: using '\Users\dbickel/R/win-library/2.11' Error i...

...n the granges For example, assuming all_genes_gr is a ~50000 genes genomic range, the result I want like belows: gene_nameupstream_genedownstream_geneoverlapped_gene gene1NAgene2NA gene2gene1gene4gene3 gene3gene1gene4gene2 gene4gene3gene5NA Currently , the strategy I use is like that, library(GenomicRanges) find_overlapped_gene <- function(idx, all_genes_gr) { #cat(idx, "\n") curr_gene <- all_genes_gr[idx] other_genes <- all_genes_gr[-idx] n <- countOverlaps(curr_gene, other_genes) gene <- subsetByOverlaps(curr_gene, other_genes) return(list(n, gene)) }? system.t...

...packages", "http://cran.rstudio.com")) That returns this Warning in install.packages : package ?tcltk? is not available (for R version 3.3.3) Warning in install.packages : package ?tcltk? is a base package, and should not be updated Warning in install.packages : dependencies ?GenomicRanges?, ?Rcompression? are not available Warning in install.packages : unable to access index for repository http://rstudio.org/_packages/bin/windows/contrib/3.3: cannot open URL 'http://rstudio.org/_packages/bin/windows/contrib/3.3/PACKAGES [[alternative HTML version deleted]]

Hello, I've been attempting to make a generic method that dispatches on the first argument, which can be either an S3 or an S4 class. This is as far as I've gotten. Any suggestions about what to try next ? library(aroma.affymetrix) library(GenomicRanges) setGeneric("analyse", function(x, y, ...) standardGeneric("analyse")) setMethodS3("analyse", "AffymetrixCelSet", function(x, y, z, ...) { x; UseMethod("analyse") } ) setGeneric("analyse") setMethod("analyse", "GRanges...

...ried patching methods to use .BasicFunsList directly as in setMethod? On Wed, Jan 21, 2015 at 10:41 AM, Peter Haverty <haverty.peter at gene.com> wrote: > Hi all, > > The function call series genericForPrimitive -> .findBasicFuns -> .findAll > happens 4400 times while the GenomicRanges package is loading. Each time > .findAll follows a chain of environments to determine that the methods > namespace is the only one that holds a variable called .BasicFunsList. This > accounts for ~10% of package loading time. I'm sure there is some history > to that design, but wou...

...tart" and "End" of two data set , ? I want to find which row (preciously "Feature") of data_2 is in every range ( between "Start" and "End") of data_1 ? Also "Chromosome" column element should be match between two data set.? I have tried "GenomicRanges" packages describe in the post ? https://stackoverflow.com/questions/11892241/merge-by-range-in-r-applying-loops But i was not successful. Can any one please help me to do this fast, as the data is very big ?? Thanks in advance. Regards............. Tanvir Ahamed Stockholm, Sweden???? |??mas...

Hi All, I have an CBS segmentation algorithm output for 10 tumor samples each from 2 different tumors. Now, I am in an urgent need to assign gene (followed by all genes present) that belong to a particular segment after I removed all the CNVs from segment data. The format of the data is: Sample Chromosome Start End Num_Probes Segment_Mean Sample1A-TA 1 51598 76187 15

...;> On Wed, Jan 21, 2015 at 10:41 AM, Peter Haverty <haverty.peter at gene.com> >> wrote: >>> >>> Hi all, >>> >>> The function call series genericForPrimitive -> .findBasicFuns -> >>> .findAll >>> happens 4400 times while the GenomicRanges package is loading. Each time >>> .findAll follows a chain of environments to determine that the methods >>> namespace is the only one that holds a variable called .BasicFunsList. >>> This >>> accounts for ~10% of package loading time. I'm sure there is some...

...tudio.com")) > >That returns this > >Warning in install.packages : > package ?tcltk? is not available (for R version 3.3.3) >Warning in install.packages : > package ?tcltk? is a base package, and should not be updated >Warning in install.packages : > dependencies ?GenomicRanges?, ?Rcompression? are not available >Warning in install.packages : > unable to access index for repository >http://rstudio.org/_packages/bin/windows/contrib/3.3: >cannot open URL >'http://rstudio.org/_packages/bin/windows/contrib/3.3/PACKAGES > > [[alternative HTML version...

...hat returns this >> >>Warning in install.packages : >> package ?tcltk? is not available (for R version 3.3.3) >>Warning in install.packages : >> package ?tcltk? is a base package, and should not be updated >>Warning in install.packages : >> dependencies ?GenomicRanges?, ?Rcompression? are not available >>Warning in install.packages : >> unable to access index for repository >>http://rstudio.org/_packages/bin/windows/contrib/3.3: >>cannot open URL >>'http://rstudio.org/_packages/bin/windows/contrib/3.3/PACKAGES >> >>...

....983 0.097 1.079 Given modern hardware capabilities and the need to efficiently load software for the user to be able to do something, perhaps we should bump the default settings so that the GC is fired sparingly when loading a large package. For users of Bioconductor, we see this for library(GenomicRanges): used (Mb) gc trigger (Mb) max used (Mb) Ncells 1322124 70.7 47185920 2520 15591302 832.7 Vcells 1216015 9.3 268435456 2048 13992181 106.8 So perhaps that user would want 900 MB of N and 100 MB of V as the trigger (corresponding to --min-vsize=100M --min-nsize=16M). Thoughts? [...

...For example, assuming all_genes_gr is a ~50000 genes genomic range, the result I want like belows: gene_name upstream_gene downstream_gene overlapped_gene gene1 NA gene2 NA gene2 gene1 gene4 gene3 gene3 gene1 gene4 gene2 gene4 gene3 gene5 NA Currently , the strategy I use is like that, library(GenomicRanges) find_overlapped_gene <- function(idx, all_genes_gr) { #cat(idx, "\n") curr_gene <- all_genes_gr[idx] other_genes <- all_genes_gr[-idx] n <- countOverlaps(curr_gene, other_genes) gene <- subsetByOverlaps(curr_gene, other_genes) return(list(n, gene)) }? system....