[Bioc-devel] Possible need for a GenomicIntersection package

Koustav Pal kou@t@v@p@| @end|ng |rom ||om@eu
Tue Jun 4 18:43:14 CEST 2019

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.pal using ifom.eu

> On 4 Jun 2019, at 18:08, Éric Fournier <Fournier.Eric.2 using 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
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