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Change values of HiC map.

Source: R/SwitchMatrix.R
SwitchMatrix.Rd

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

Usage

SwitchMatrix(hicLst, matrixKind = c("obs", "norm", "o/e", "exp"))

Arguments

hicLst

<ListContactMatrix>: The HiC maps list.

matrixKind

: 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(
        interactionType = "cis",
        method = "ICE"
    ) |>
    OverExpectedHiC()


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