findDMCs-method: findDMCs method

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

findDMCs method

Description

finds the DMCs after smoothing using HMM

Usage

findDMCs(
  object,
  formula,
  FDRthreshold,
  Methylthreshold,
  mc.cores,
  windowsize,
  weightfunction
)

## S4 method for signature 'BSDMCs'
findDMCs(
  object,
  formula,
  FDRthreshold,
  Methylthreshold,
  mc.cores,
  windowsize,
  weightfunction
)

Arguments

object	A BSData-class or BSDMCs-class object
formula	A formula
FDRthreshold	A numeric value
Methylthreshold	A positive numeric value; the default is 0.001
mc.cores	An integer greater than 0
windowsize	An integer value for partitioning data into windows of size windowsize.
weightfunction	A function to create weights using variance obtained form the MCMC algorithm

Value

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)
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)
OBJ3 <- methHMMCMC(OBJ2, mc.cores=2)
OBJ4 <- findDMCs(OBJ3, mc.cores=2)
head(metadata(OBJ4)$DMCHMM)

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