Description Arguments Value Slots Author(s) Examples

The `BSDMCs`

object is an S4 class that represents
differentially methylated CpG sites (DMCs) in BS-Seq Data.

`methReads` |
The matrix |

`totalReads` |
The matrix |

`methLevels` |
The matrix |

`methStates` |
The matrix |

`methVars` |
The matrix |

A `BSDMCs-class`

object

`methReads`

An integer matrix

`totalReads`

An integer matrix

`methLevels`

A numeric matrix

`methStates`

An integer matrix

`methVars`

A double matrix

Farhad Shokoohi <[email protected]>

1 2 3 4 5 6 7 8 9 10 11 12 | ```
nr <- 500; nc <- 16
metht <- matrix(as.integer(runif(nr * nc, 0, nr)), 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 <- cBSDMCs(rowRanges=r1,methReads=methc,totalReads=metht,
methLevels=methl,methStates=meths,methVars=methv,colData=cd1)
OBJ2
``` |

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