plotDMCFB-method: plotDMCFB method

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

plotDMCFB method

Description

Plotting the results of DMC identifation stored in a BSDMC-class object

Usage

plotDMCFB(object, region, nSplit, parList)

## S4 method for signature 'BSDMC'
plotDMCFB(object, region, nSplit, parList)

Arguments

object	A BSDMC-class object
region	An integer vector of length two specifying which subset of the object to be plotted
nSplit	A integer value specifying the number of subsets must be done for plotting the results of DMC identification
parList	A list specifying plots parameters, see par

Value

Plot

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
)
plotDMCFB(OBJ2)

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