BSDMCs-class {DMCHMM} | R Documentation |
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 |
A BSDMCs-class
object
methReads
An integer matrix
totalReads
An integer matrix
methLevels
A numeric matrix
methStates
An integer matrix
Farhad Shokoohi <shokoohi@icloud.com>
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 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,colData=cd1) OBJ2