When it comes to Hi-C, HiCBricks which is a package that I authored already incorporates some of the intersection capabilities you are asking for. The functions of interest are Brick_return_region_position and Brick_fetch_range_index. These functions take genomic coordinates and return intersections against the genomic coordinates associated to a Hi-C matrix.
Koustav Pal, PhD Post-Doctoral Fellow in Genome Architecture, Computational Genomics Group, IFOM - The FIRC Institute of Molecular Oncology, Via Adamello 16, 20139 Milano, Italy. Phone: +393441130157 E-mail: koustav....@ifom.eu > On 4 Jun 2019, at 18:08, Éric Fournier > <fournier.eri...@crchudequebec.ulaval.ca> wrote: > > Hi, > > in a lot of the bioinformatics analysis I have to carry out, I end up needing > to take an arbitrary number of GRanges objects and flatten them before > generating a matrix of all elements that overlap. This is useful for, say, > comparing replicates in a ChIP-seq experiment, or caracterizing the types of > interactions in a HiC or ChIA-PET experiment. As such, I've written quite a > few utility functions around that concept, for example to generate Venn plots > of the intersections, querying specific intersections, or plotting heatmaps > of correlation. > > My question is two-fold: are there already existing packages that already > incorporate some of that core functionality, and if not, would repackaging > those functions as a package be of interest to the Bioconductor community at > large? > > Thank you for your time, > -Eric Fournier > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
