findDMCFB-method: findDMCFB method

In shokoohi/DMCFB: Differentially Methylated Cytosines via a Bayesian Functional Approach

findDMCFB method

Description

DMC identification via Bayesian functional regression models

Usage

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 <[e-mail]>

Examples

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

shokoohi/DMCFB documentation built on April 21, 2022, 5:53 a.m.