methLevels-method: methLevels method

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

methLevels method

Description

Returns methLevels stored in BSDMCs-class

Assigns methLevels to BSDMCs-class

Usage

methLevels(object)

methLevels(object) <- value

## S4 method for signature 'BSDMCs'
methLevels(object)

## S4 replacement method for signature 'BSDMCs,matrix'
methLevels(object) <- value

Arguments

object	A BSData-class or BSDMCs-class object
value	An integer matrix

Value

A matrix

A BSDMCs-class object

Author(s)

Farhad Shokoohi <[e-mail]>

Examples

set.seed(1980)
nr <- 150; nc <- 8
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), 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)
methLevels(OBJ2)
methLevels(OBJ2) <- methl

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