VSS-Hi-C: variance-stabilized signals for chromatin contacts

The genome-wide chromosome conformation capture assay Hi-C is widely used to study chromatin 3D structures and their functional implications. Read counts from Hi-C indicate the strength of chromatin contact between each pair of genomic loci. These read counts are heteroskedastic: that is, a difference between the interaction frequency of 0 and 100 is much more significant than a difference between the interaction frequency of 1000 and 1100. This property impedes visualization and downstream analysis because it violates the Gaussian variable assumption of many computational tools. Thus heuristic transformations aimed at stabilizing the variance of signals like the shifted-log transformation are typically applied to data before its visualization and inputting to models with Gaussian assumption. However, such heuristic transformations cannot fully stabilize the variance because of their restrictive assumptions about the mean-variance relationship in the data.

Here, we present VSS-Hi-C, a data-driven variance stabilization method for Hi-C data. We show that VSS-Hi-C signals have a unit variance improving visualization of Hi-C, for example in heatmap contact maps. VSS-Hi-C signals also improve the performance of subcompartment callers relying on Gaussian observations. VSS-Hi-C is implemented as an R package and can be used for variance stabilization of different genomic and epigenomic data types with two replicates available.

https://github.com/nedashokraneh/vssHiC.