Description Usage Arguments Details Value References Examples

Train the smoothing parameter (neighborhood size).

1 |

`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. |

`max` |
An integer indicating the maximum distance of interaction that is considered. |

`range` |
A vector of consecutive integers from which the optimal smoothing parameter is searched, starting from zero (i.g., 0:10). |

A fraction (10%) of data are first randomly sampled, then
the scc for the sampled data is computed at a series of smoothing
parameterts in the ascending order. The samllest h at which the increment
of scc is less than 0.01 is saved. This procedure is repeat 10 times, and
the mode of the 10 `h`

's is outputed as the estimated optimal
neighborhood size.

a integer estimated to be the optimal smoothing parameter.

HiCRep: 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.

1 2 3 |

```
smoothing:0
smoothing:1
```

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