cBSDMC-method {DMCFB} | R Documentation

## cBSDMC method

### Description

Creates a `BSDMC-class` object

### Usage

    cBSDMC(
      methReads,
      totalReads,
      methLevels,
      rowRanges,
      colData = DataFrame(row.names = colnames(methReads)),
      metadata = list(),
      ...
    )

    ## S4 method for signature 'matrix,matrix,matrix,GRanges'
    cBSDMC(
      methReads,
      totalReads,
      methLevels,
      rowRanges,
      colData = DataFrame(row.names = colnames(methReads)),
      metadata = list(),
      ...
    )

### Arguments

`methReads` | The matrix `methReads` contains the number of methylated reads spanning a CpG-site. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`totalReads` | The matrix `totalReads` contains the number of reads spanning a CpG-site. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`methLevels` | The matrix `methLevels` contains the predicted methylation level spanning a CpG-site using Bayesian functional regression models. The rows represent the CpG sites in `rowRanges` and the columns represent the samples in `colData`.
`rowRanges` | A `GRanges` or `GRangesList` object describing the ranges of interest. Names, if present, become the row names of the `SummarizedExperiment` object. The length of the `GRanges` or `GRangesList` must equal the number of rows of the matrices in `assays`. If `rowRanges` is missing, a `SummarizedExperiment` instance is returned.
`colData` | Object of class `'DataFrame'` containing information on variable values of the samples
`metadata` | A `list` of storing MCMC samples or DMCs
`...` | other possible parameters

### Details

The rows of a `BSDMC` object represent ranges (in genomic coordinates) of interest. The ranges of interest are described by a `GRanges` or a `GRangesList` object, accessible using the `rowRanges` function. The `GRanges` and `GRangesList` classes contains sequence (e.g., chromosome) name, genomic coordinates, and strand information. Each range can be annotated with additional data; this data might be used to describe the range or to summarize results (e.g., statistics of differential abundance) relevant to the range. Rows may or may not have row names; they often will not.

### Value

A `BSDMC-class`

### Author(s)

Farhad Shokoohi <shokoohi@icloud.com>

### Examples

    set.seed(1980)
    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)
    meths <- matrix(as.integer(runif(nr * nc, 0, 10)), nr)
    methl <- methc / metht
    methv <- matrix((runif(nr * nc, 0.1, 0.5)), nr)
    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]
    )
    OBJ2 <- cBSDMC(
      rowRanges = r1, methReads = methc, totalReads = metht,
      methLevels = methl, methStates = meths, methVars = methv, colData = cd1
    )
    OBJ2

[Package DMCFB version 1.4.0 Index]