Question: Representing Interaction Data Using Iranges/Granges For 5C/Hi-C Data Analysis
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gravatar for Naveen
8.6 years ago by
Naveen10
Naveen10 wrote:

I am trying to represent a large (many million entries) interaction matrix between genomic loci, possibly on different chromosomes. These matrices are generally the results of 5C/Hi-C type experiments.

Q: is there an existing data structure based on IRanges that does something like that?

In essence each entry would consist of two genomic ranges, one for the source and one for the target, possibly with a frequency field showing how many times this interaction was sequenced. I used simple data frames so far, which serves the purpose, but might not be the most efficient in terms of storage.

R bioconductor • 1.7k views
ADD COMMENTlink modified 7.1 years ago by Biostar ♦♦ 20 • written 8.6 years ago by Naveen10

afaik it is not possible to link IRanges objects that way, but prove me wrong. What you needed was a link between two single Ranges entries, you could make a separate interaction matrix instead containing the indices as integer values of corresponding RangedData lines in 2 columns (similar to a matchMatrix from computeOverlaps)

ADD REPLYlink written 8.6 years ago by Michael Dondrup47k
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