BSData-class: BSData object

Description Arguments Value Slots Author(s) See Also Examples

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 <[email protected]>

See Also

SummarizedExperiment objects.

Examples

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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 Sept. 6, 2018, 1:55 p.m.