prep: Pre-processing the Hi-C matrices

In qunhualilab/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)

qunhualilab/hicrep documentation built on Feb. 27, 2020, 9:17 p.m.