getSigRegion: Obtain the significant DMRs.

In boyinggong/methcp: Differential methylation anlsysis for bisulfite sequencing data

Description

getSigRegion returns the significant DMRs giving the segmented MethCP object.

Usage

getSigRegion(
    object, sig.level = 0.01, mean.coverage = 1,
    mean.diff = 0.1, nC.valid = 10)

Arguments

object	a MethCP object that is segmented using function segmentMethCP.
sig.level	significance level to call a region DMR.
mean.coverage	The minimum average coverage required for the reported DMRs.
mean.diff	The minimum differences between groups required for the reported DMRs.
nC.valid	number of valid cytosines required for the reported DMRs.

Value

a data.frame containing the DMRs.

Examples

library(bsseq)
# Simulate a small dataset with 2000 cyotsine and 6 samples,
# 3 in the treatment group and 3 in the control group. The
# methylation ratio are generated using Binomial distribution
# with probability 0.3.
nC <- 2000
sim_cov <- rnbinom(6*nC, 5, 0.5) + 5
sim_M <- vapply(
    sim_cov, function(x) rbinom(1, x, 0.3), FUN.VALUE = numeric(1))
sim_cov <- matrix(sim_cov, ncol = 6)
sim_M <- matrix(sim_M, ncol = 6)
# methylation ratios in the DMRs in the treatment group are
# generated using Binomial(0.7)
DMRs <- c(600:622, 1089:1103, 1698:1750)
sim_M[DMRs, 1:3] <- vapply(
    sim_cov[DMRs, 1:3], function(x) rbinom(1, x, 0.7),
    FUN.VALUE = numeric(1))
# sample names
sample_names <- c(paste0("treatment", 1:3), paste0("control", 1:3))
colnames(sim_cov) <- sample_names
colnames(sim_M) <- sample_names

# create a bs.object
bs_object <- BSseq(gr = GRanges(
    seqnames = "Chr01",
    IRanges(start = (1:nC)*10, width = 1)),
    Cov = sim_cov, M = sim_M, sampleNames = sample_names)
DMRs_pos <- DMRs*10
methcp_obj1 <- calcLociStat(
    bs_object,
    group1 = paste0("treatment", 1:3),
    group2 = paste0("control", 1:3),
    test = "methylKit")
methcp_obj1 <- segmentMethCP(
    methcp_obj1, bs_object,
    region.test = "fisher")
methcp_res1 <- getSigRegion(methcp_obj1)

boyinggong/methcp documentation built on April 25, 2021, 9 a.m.