BiSeq (version 1.12.0)

compareTwoSamples: Detects DMRs by comparing two samples

Description

Determines the differences of (smoothed) methylation levels between two samples and aggregates the sites surpassing a minimum difference to DMRs.

Usage

compareTwoSamples(object, sample1, sample2, minDiff, max.dist)

Arguments

object

A BSrel.

sample1

A numeric or character specifying the first sample to be used.

sample2

A numeric or character specifying the second sample to be used.

minDiff

A numeric greater than 0 and smaller or equal to 1.

max.dist

Numeric. The maximum distance between two CpG sites (or grid points) with absolute methylation differences greater or equal than minDiff in a DMR. If grid points are used: should be the same as grid.dist in predictMeth.

Value

A GRanges object.

Details

This function determines the differences between the methylation levels of sample1 and sample2 for each site. Successive sites with methylation differences smaller or equal to minDiff are summarized.

See Also

predictMeth

Examples

data(rrbs)
rrbs <- rrbs[, c(1,6)]
CpG.clusters <- clusterSites(object = rrbs, perc.samples = 1,
                             min.sites = 20, max.dist = 100)
predictedMeth <- predictMeth(object = CpG.clusters)
DMRs <- compareTwoSamples(predictedMeth, sample1 = 1, sample2 = 2,
                          minDiff = 0.3, max.dist = 100)