Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`

Hi Michael, Thank you for the pointer to plyranges - looks very useful! > Maybe a better name is "straddle" for when ranges > straddle one of the endpoints? In keeping with the current pattern of > Ranges API, there would be a single function: straddle(x, side, left, > right, ignore.strand=FALSE)

Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`

Hmm no that wouldn't work, it would become messy trying to figure out when incompatible arguments are provided. Aditya From: Bioc-devel [bioc-devel-boun...@r-project.org] on behalf of Bhagwat, Aditya [aditya.bhag...@mpi-bn.mpg.de] Sent: Monday, Septemb

Re: [Bioc-devel] Error in HDF5 - Package submission - Not detected locally

Hi Tiago, I suspect what has happened here is that when create the mini_pbmc3k object, you're doing this by subsetting the PBMC, 3k scRNA-seq data from ExperimenHub. The assay data for that are are actually stored in an HDF5 file which will be downloaded and stored in your ExperimentHub cache on y

Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`

Michael, actually, such a generic straddle() could be useful: straddle(leftstart=-100, rightend=100) # extended range straddle(leftstart=-100, leftend=-1) # left flank straddle(rightstart=1, rightend=100) # right flank straddle(leftstart=-100, leftend=-1, rightstart=1, rightend=100) # l

Re: [Bioc-devel] Error in HDF5 - Package submission - Not detected locally

Hello Mike, Thank you for the detailed explanation. You are right, for the vignette, I can download it from the ExperimentHub subset the pbmc3k dataset in the first few lines. The main point of having a new dataset was to use it in the examples of functions. The full dataset is too big and the ex

Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`

It's on the right track. The case where two ranges are produced is problematic, because we would want this to be a parallel vector operation, where the length of the input is the same as the length of the output. So that last case I think might just ignore the leftend and rightstart arguments with

[Bioc-devel] Fwd: TissueEnrich problems reported in the Multiple platform build/check report for BioC 3.9

Hi All, I just got the message that my package is giving an error during the build process on Bioconductor build server. I saw the logs and found it is failing while building the vignette. I am not sure why it's happening as I have not updated the package since release and it was building without

[Bioc-devel] Bioconductor 3.10 release schedule

Hi Bioconductor Community, The release of Bioconductor 3.10 will be on Wednesday October 30. Some key dates can be found on the website release schedule page: http://bioconductor.org/developers/release-schedule/ Bioconductor - Release: Schedule

[Bioc-devel] New Package Submission Deadline for Bioc Release 3.10

The final day to submit new packages to the Bioconductor contributions tracker to have a shot at being included in the upcoming 3.10 release is Friday October 4th. Please note: submission by this date does not guarantee it will be included - the package must undergo an official review and be ac

Re: [Bioc-devel] Error in HDF5 - Package submission - Not detected locally

Hi Tiago, The following will create a similarly sized subset of the PBMC3k dataset with the counts in-memory as a sparse matrix: pbmc3k <- TENxPBMCData::TENxPBMCData("pbmc3k") mini_pbmc3k <- pbmc3k[1:1700, 1:600] assay(mini_pbmc3k) <- as(assay(mini_pbmc3k), "dgCMatrix") Cheers, Pete On Mon, 16

Re: [Bioc-devel] Error in HDF5 - Package submission - Not detected locally

Hi Tiago, On 9/16/19 06:35, Tiago Lubiana Alves wrote: > Hello Mike, > > Thank you for the detailed explanation. > > You are right, for the vignette, I can download it from the ExperimentHub > subset the pbmc3k dataset in the first few lines. The main point of having > a new dataset was to use i

Re: [Bioc-devel] Extending GenomicRanges::`intra-range-methods`

Hi Aditya, I think straddle would be a great addition to plyranges. Happy for you to put in a PR and add you as a contributor. Maybe instead of specifying the start etc. we could dispatch on anchored ranges instead? So we’d follow the anchor_start(gr) %>% straddle(). We could also have the dir