methLevels-method: methLevels method

Description Usage Arguments Value Author(s) Examples

Description

Returns methLevels stored in BSDMCs-class

Assigns methLevels to BSDMCs-class

Usage

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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 <[email protected]>

Examples

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