findDMCFB-method: findDMCFB method

Description Usage Arguments Value Author(s) Examples

Description

DMC identification via Bayesian functional regression models

Usage

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findDMCFB(
  object,
  bwa,
  bwb,
  nBurn,
  nMC,
  nThin,
  alpha,
  sdv,
  nCores,
  pSize,
  sfiles
)

## S4 method for signature 'BSDMC'
findDMCFB(
  object,
  bwa,
  bwb,
  nBurn,
  nMC,
  nThin,
  alpha,
  sdv,
  nCores,
  pSize,
  sfiles
)

Arguments

object

A BSDMC-class object

bwa

An integer value specifying the band-width size of B-spline basis matrix for a natural cubic spline for the group-specific effects of the Bayesian functional regression model

bwb

An integer value specifying the band-width size of B-spline basis matrix for a natural cubic spline for the individual-specific effects of the Bayesian functional regression model

nBurn

An integer value specifying the number of burn-in samples

nMC

An integer value specifying the number of MCMC samples after burn-in

nThin

An integer value specifying the thining number in MCMC

alpha

A numeric value specifying the level of α in credible interval (1-α)\%

sdv

An double value specifying the standard deviation of priors

nCores

An integer value specifying the number of machine cores for parallel computing

pSize

An integer value specifying the number of cytosines in a regrion to be used in a Bayesian functiona regression model for DMC detection

sfiles

A logical value indicating whether files to be saved or not.

Value

BSDMC-class object

Author(s)

Farhad Shokoohi <shokoohi@icloud.com>

Examples

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set.seed(1980)
nr <- 1000
nc <- 4
metht <- matrix(as.integer(runif(nr * nc, 0, 100)), nr)
methc <- matrix(rbinom(n = nr * nc, c(metht), prob = runif(nr * nc)), nr, nc)
methl <- methc / metht
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 <- cBSDMC(
  rowRanges = r1, methReads = methc, totalReads = metht,
  methLevels = methl, colData = cd1
)
OBJ2 <- findDMCFB(OBJ1,
  bwa = 10, bwb = 10, nBurn = 50, nMC = 50, nThin = 1,
  alpha = 0.05, nCores = 2, pSize = 500, sfiles = FALSE
)
OBJ2

DMCFB documentation built on Nov. 8, 2020, 8:03 p.m.