totalReads-method: totalReads method

In DMCHMM: Differentially Methylated CpG using Hidden Markov Model

Description

Returns totalReads stored in BSData-class

Assigns totalReads to BSData-class

Returns totalReads stored in BSDMCs-class

Assigns totalReads to BSDMCs-class

Usage

totalReads(object)

totalReads(object) <- value

totalReads(object)

totalReads(object) <- value

## S4 method for signature 'BSData'
totalReads(object)

## S4 replacement method for signature 'BSData,matrix'
totalReads(object) <- value

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

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

Arguments

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

Value

A matrix

A BSData-class object

A matrix

A BSDMCs-class object

Author(s)

Farhad Shokoohi <[e-mail]>

Examples

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)
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)
totalReads(OBJ1)
totalReads(OBJ1) <- metht

DMCHMM documentation built on Nov. 8, 2020, 8:20 p.m.