methLevels-method {DMCFB} | R Documentation

## methLevels method

### Description

Returns `methLevels` stored in `BSDMC-class`

Assigns `methLevels` to `BSDMC-class`

### Usage

    methLevels(object)

    methLevels(object) <- value

    ## S4 method for signature 'BSDMC'
    methLevels(object)

    ## S4 replacement method for signature 'BSDMC,matrix'
    methLevels(object) <- value

### Arguments

`object` | A `BSDMC-class` object
`value` | An integer matrix

### Value

A matrix

A `BSDMC-class` object

### Author(s)

Farhad Shokoohi <shokoohi@icloud.com>

### Examples

    nr <- 150
    nc <- 8
    metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
    methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
    methl <- methc / metht
    r1 <- GRanges(rep("chr1", nr), IRanges(1:nr, width = 1), strand = "*")
    names(r1) <- 1:nr
    cd1 <- DataFrame(
      Group = rep(c("G1", "G2"), each = nc / 2),
      row.names = LETTERS[1:nc]
    )
    OBJ1 <- cBSDMC(
      rowRanges = r1, methReads = methc, totalReads = metht,
      methLevels = methl, colData = cd1
    )
    methLevels(OBJ1)
    methLevels(OBJ1) <- methl

[Package DMCFB version 1.4.0 Index]