prep {hicrep} | R Documentation |
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.
prep(R1, R2, resol, h, max)
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. |
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.
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.
data(HiCR1) data(HiCR2) processed <- prep(HiCR1, HiCR2, 1000000, 0, 5000000) head(processed)