Compute Vanilla Count Correction.

Compute Vanilla Count or Vanilla Count square root correction normalization on hic maps.

Usage

VCnorm(hic.cmx = NULL, qtlTh.num = 0.15, sqrt.bln = TRUE)

Arguments

hic.cmx

<contactMatrix>: The HiC maps chunk to normalize.

qtlTh.num

<numerical>: The threshold quantile below which the bins will be ignored. (Default 0.15)

sqrt.bln

<logical>: Whether the square root must be apply. (Default TRUE)

Value

A matrices list.

Details

VCnorm

Examples

# Data
data(HiC_Ctrl.cmx_lst)

HiC_Ctrl_VC.cmx <- VCnorm(HiC_Ctrl.cmx_lst[["2L_2L"]])
HiC_Ctrl_VC_SQRT.cmx <- VCnorm(HiC_Ctrl.cmx_lst[["2L_2L"]], sqrt.bln = TRUE)