methHMEM-method: methHMEM method

methHMEM-methodR Documentation

methHMEM method

Description

Estimates the HMM methylation paths and the HMM order for each sample using the EM algorithm

Usage

methHMEM(object, MaxK, MaxEmiter, epsEM, useweight, mc.cores)

## S4 method for signature 'BSData'
methHMEM(object, MaxK, MaxEmiter, epsEM, useweight, mc.cores)

Arguments

object

A BSData-class or BSDMCs-class object

MaxK

An integer value

MaxEmiter

An integer value

epsEM

A positive numeric value

useweight

A logical value

mc.cores

An integer greater than 0

Value

BSDMCs-class object

Author(s)

Farhad Shokoohi <shokoohi@icloud.com>

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)
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)
OBJ2 <- methHMEM(OBJ1, MaxK=2, mc.cores=2)
OBJ2

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