dmrFinder {bsseq} | R Documentation

## Finds differentially methylated regions for whole genome bisulfite sequencing data.

### Description

Finds differentially methylated regions for whole genome bisulfite sequencing data. Essentially identifies regions of the genome where all methylation loci have an associated t-statistic that is beyond a (low, high) cutoff.

### Usage

    dmrFinder(bstat, cutoff = NULL, qcutoff = c(0.025, 0.975),
      maxGap=300, stat = "tstat.corrected", verbose = TRUE)

### Arguments

`bstat` | An object of class `BSseqStat` or `BSseqTstat`.
`cutoff` | The cutoff of the t-statistics. This should be a vector of length two giving the (low, high) cutoff. If `NULL`, see `qcutoff`.
`qcutoff` | In case `cutoff` is `NULL`, compute the cutoff using these quantiles of the t-statistic.
`maxGap` | If two methylation loci are separated by this distance, break a possible DMR. This guarantees that the return DMRs have CpGs that are this distance from each other.
`stat` | Which statistic should be used?
`verbose` | Should the function be verbose?

### Details

The workhorse function is `BSmooth.tstat` which sets up a t-statistic for a comparison between two groups.

Note that post-processing of these DMRs are likely to be necessary, filtering for example for length (or number of loci).

### Value

A `data.frame` with columns

`start,end,width,chr` | genomic locations and width.
`n` | The number of methylation loci.
`invdensity` | Average length per loci.
`group1.mean` | The mean methylation level across samples and loci in 'group1'.
`group2.mean` | The mean methylation level across samples and loci in 'group2'.
`meanDiff` | The mean difference in methylation level; the difference between `group1.mean` and `group2.mean`.
`idxStart, idxEnd, cluster` | Internal use.
`areaStat` | The 'area' of the t-statistic; equal to the sum of the t-statistics for the individual methylation loci.
`direction` | either ‘hyper’ or ‘hypo’.
`areaStat.corrected` | Only present if `column = "tstat.corrected"`, contains the area of the corrected t-statistics.

### Author(s)

Kasper Daniel Hansen khansen@jhsph.edu.

### References

KD Hansen, B Langmead, and RA Irizarry. BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biology (2012) 13:R83. doi:10.1186/gb-2012-13-10-r83.

### See Also

`BSmooth.tstat` for the function constructing the input object, and `BSseqTstat` for its class. In the example below, we use `BS.cancer.ex.tstat` as the actual input object. Also see the package vignette(s) for a detailed example.

### Examples

    if(require(bsseqData)) {
      dmrs0 <- dmrFinder(BS.cancer.ex.tstat, cutoff = c(-4.6, 4.6), verbose = TRUE)
      dmrs <- subset(dmrs0, abs(meanDiff) > 0.1 & n >= 3)
    }

[Package bsseq version 1.18.0 Index]