BSData-class: BSData object

In shokoohi/DMCHMM: Differentially Methylated CpG using Hidden Markov Model

BSData object

Description

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

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.

Value

A BSData-class object

Slots

methReads

An integer matrix

totalReads

An integer matrix

Author(s)

Farhad Shokoohi <[e-mail]>

See Also

SummarizedExperiment objects.

Examples

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

shokoohi/DMCHMM documentation built on April 19, 2022, 3:25 a.m.