hicrep-package: HiCRep pipeline calculates reproducibility of Hi-C...

In hicrep: Measuring the reproducibility of Hi-C data

Description

The pipelne is a two-step method. The first step is to smooth the Hi-C matrix, and the #' second step is to calculate the stratum-adjusted correlation coefficient (scc). The method also provides the estimation of asymptotic standard deviation of scc.

Details

• Package: hicrep

• Type: Package

• Version: 0.99.6

• Date: 2017-2-5

• License: GPL-2

• LazyLoad: Yes

The main functions are prep, get.scc and htrain. The function prep will take the two replicates of N*(3+N) matrix format as input, and return the vectorized, smoothed or unsmoothed (when smoothing neighborhood size parameter h = 0) Hi-C data, which will subsequently used to compute stratum-adjusted correlation coefficients (scc). The function get.scc computes scc and its asymptotic standard deviation, and the function htrain estimates optimal smoothing neighborhood size from the input matrices.

Author(s)

Tao Yang Maintainer: Tao Yang <[e-mail]>

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)

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

scc.out <- get.scc(processed, 1000000, 5000000)
scc.out$scc
scc.out$std

Example output

smoothing:0
smoothing:1
smoothing:2
Warning message:
In htrain(HiCR1, HiCR2, 1e+06, 5e+06, 0:2) :
  Note: It's likely that your searching range is too narrow. 
                    Try to expand the range and rerun it
          [,1]
[1,] 0.9720146
[1] 0.006901945

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