Apply a matrix-balancing normalization method to a list of contacts matrix.
Usage
BalanceHiC(
hic.cmx_lst,
method.chr = "ICE",
interaction.type = NULL,
maxIter.num = 50,
qtlTh.num = 0.15,
cores.num = 1,
verbose.bln = FALSE
)Arguments
- hic.cmx_lst
<List[contactMatrix]>: The HiC maps list.
- method.chr
<character> : The kind of normalization method. One of "ICE", "VC" or "VC_SQRT" (Default "ICE")
- interaction.type
<character> : "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.num
<numerical>: The maximum iteration number.
- qtlTh.num
<numerical>: The threshold quantile below which the bins will be ignored. (Default 0.15)
- cores.num
<numerical> : Number of cores to be used. (Default 1)
- verbose.bln
<logical>: If TRUE show the progression in console. (Default FALSE)
Examples
data(HiC_Ctrl.cmx_lst)
HiC_Ctrl_ICE.cmx_lst <- BalanceHiC(HiC_Ctrl.cmx_lst,
interaction.type = "cis",
method.chr = "ICE"
)
#> 2L_2R remove from output.
HiC_Ctrl_VC.cmx_lst <- BalanceHiC(HiC_Ctrl.cmx_lst,
interaction.type = c("cis", "trans"),
method.chr = "VC"
)
HiC_Ctrl_VC_SQRT.cmx_lst <- BalanceHiC(HiC_Ctrl.cmx_lst,
interaction.type = "all",
method.chr = "VC_SQRT"
)