dmrFinder: Finds differentially methylated regions for whole genome...

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

View source: R/dmrFinder.R

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

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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 [email protected].

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

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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)
}

Example output

Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians


Attaching package: 'DelayedArray'

The following objects are masked from 'package:matrixStats':

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following object is masked from 'package:base':

    apply

Loading required package: bsseqData
Warning message:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'bsseqData'

bsseq documentation built on Nov. 1, 2018, 3:32 a.m.