prep: Pre-processing the Hi-C matrices

In hicrep: Measuring the reproducibility of Hi-C data

Description

Format pairs of Hi-C matrices, smooth the matrices with matrix resolution, and maximum distance of interaction considering specified by user, filter out the bins that has no reads in both replciates.

Usage

prep(R1, R2, resol, h, max)

Arguments

R1	a Hi-C intra-chromosome matrix.
R2	the other intra-chromosome matrix to compare with.
resol	an integer indicating the resolution of the Hi-C matrix.
h	an integer indicating the size of the smoothing neighborhood.
max	an integer indicating the maximum distance of interaction that is considered.

Value

a smoothed (or not when resol = 0), zero-filtered and vectorized Hi-C data. The first two columns are bin start and bin ends, and the last two columns are reads number if replicate 1 and replicate 2 respectively.

References

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li. bioRxiv 101386; doi: https://doi.org/10.1101/101386.

Examples

data(HiCR1)
data(HiCR2)
processed <- prep(HiCR1, HiCR2, 1000000, 0, 5000000)
head(processed)

Example output

          V1       V2   V3   V4
849 16500000 16500000 2832 4636
850 16500000 17500000 2027 3204
851 16500000 18500000  358  504
852 16500000 19500000  162  247
853 16500000 20500000   68  109
854 16500000 21500000   66  129

hicrep documentation built on April 28, 2020, 7:51 p.m.