Compute HiC matrix-balancing. — BalanceHiC • HicAggR

Apply a matrix-balancing normalization method to a list of contacts matrix.

Usage

BalanceHiC(
  hicLst,
  method = "ICE",
  interactionType = NULL,
  maxIter = 50,
  qtlTh = 0.15,
  cores = 1,
  verbose = FALSE
)

Arguments

hicLst: <ListContactMatrix>: The HiC maps list.
method: : The kind of normalization method. One of "ICE", "VC" or "VC_SQRT" (Default "ICE")
interactionType: : "cis", "trans", c("cis", "trans"), "all". If NULL normalization is apply on cis contactMatrix then trans contactMatrix (equivalent to c("cis", "trans")). If is "all", normalization is apply on all contactMatrix at once. (Default NULL)
maxIter: : The maximum iteration number.
qtlTh: : The quantile threshold below which the bins will be ignored. (Default 0.15)
cores: : Number of cores to be used. (Default 1)
verbose: : If TRUE show the progression in console. (Default FALSE)

Value

A matrices list.

Details

BalanceHiC

Examples

data(HiC_Ctrl.cmx_lst)

HiC_Ctrl_ICE.cmx_lst <- BalanceHiC(HiC_Ctrl.cmx_lst,
    interactionType = "cis",
    method = "ICE"
)

HiC_Ctrl_VC.cmx_lst <- BalanceHiC(HiC_Ctrl.cmx_lst,
    interactionType = c("cis", "trans"),
    method = "VC"
)

HiC_Ctrl_VC_SQRT.cmx_lst <- BalanceHiC(HiC_Ctrl.cmx_lst,
    interactionType = "all",
    method = "VC_SQRT"
)