BSData-class: BSData object
In DMCHMM: Differentially Methylated CpG using Hidden Markov Model

Description Arguments Value Slots Author(s) See Also Examples

The BSData object is an S4 class that represents BS-Seq Data.

`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`.

A BSData-class object

methReads: An integer matrix
totalReads: An integer matrix

Farhad Shokoohi <shokoohi@icloud.com>

SummarizedExperiment objects.

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)
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<-cBSData(rowRanges=r1,methReads=methc,totalReads=metht,colData=cd1)
OBJ1