fast.mean.filter: A fast mean filter algorithm to smooth a matrix

In MonkeyLB/hicrep: Measuring the reproducibility of Hi-C data

Description

A fast mean filter algorithm to smooth a matrix

Usage

fast.mean.filter(mat, h)

Arguments

mat	the matrix to be smoothed.
h	window size used to calculate the mean for each cell.

Value

a smoothed matrix.

References

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient. Tao Yang, Feipeng Zhang, Galip Gurkan Yardimci, Fan Song, Ross C Hardison, William Stafford Noble, Feng Yue, Qunhua Li. Genome Research 2017. doi: 10.1101/gr.220640.117

Examples

data(HiCR1)
data(HiCR2)

#Estimate the optimial smoothing neighborhood size parameter
h_hat <- htrain(HiCR1, HiCR2, 1000000, 0, 5000000, 0:2)

scc.out <- get.scc(HiCR1, HiCR2, 1000000, 0)
scc.out$scc
scc.out$std

MonkeyLB/hicrep documentation built on Dec. 15, 2020, 12:47 a.m.