compareTwoSamples: Detects DMRs by comparing two samples
In BiSeq: Processing and analyzing bisulfite sequencing data

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`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`.

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.

A GRanges object.

Katja Hebestreit

predictMeth

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)