Change values of HiC map.

Change values in matrix with observed, balanced, observed/expected or expected values according to what are be done in hic.

Usage

SwitchMatrix(hic.cmx_lst, matrixKind.chr = c("obs", "norm", "o/e", "exp"))

Arguments

hic.cmx_lst

<List[contactMatrix]>: The HiC maps list.

matrixKind.chr

<character>: The kind of matrix you want.

Value

A contactMatrix list.

Details

SwitchMatrix

Examples

# Data
data(HiC_Ctrl.cmx_lst)

# Preprocess HiC
HiC.cmx_lst <- HiC_Ctrl.cmx_lst |>
    BalanceHiC(
        interaction.type = "cis",
        method.chr = "ICE"
    ) |>
    OverExpectedHiC()
#> 2L_2R remove from output.

# Switch values in matrix
HiC_Ctrl_Obs.cmx_lst <- SwitchMatrix(HiC.cmx_lst, matrixKind.chr = "obs")
HiC_Ctrl_Norm.cmx_lst <- SwitchMatrix(HiC.cmx_lst, matrixKind.chr = "norm")
HiC_Ctrl_oe.cmx_lst <- SwitchMatrix(HiC.cmx_lst, matrixKind.chr = "o/e")
#> 
#> hic.cmx_lst is already o/e.
HiC_Ctrl_exp.cmx_lst <- SwitchMatrix(HiC.cmx_lst, matrixKind.chr = "exp")