compHists {MMDiff2} | R Documentation

## Compute Peak histograms

### Description

This function computes histograms at pre-defined regions (peaks) from mapped fragments, i.e. fragment counts at genomic position. Note, in contrast to genomic coverage or density maps, this function uses a single position per fragment (usually its center) rather than the whole extend of the fragment. This results in a significant increase in resolution. The parameter `whichPos` determines whether fragment centers, start or end positions should be considered ('Center','Left','Right'). Results are stored as a list in the `Hists` slot of the DBAmmd Object, with one entry per peak. For each peak i, a (n x L_i) matrix is generated, where n is the number of samples and L_i is the number of bins used to cover the extend of the peak. Note, L_i varies between peaks of different lengths.

### Usage

    compHists(MD, bin.length = 20, whichPos = "Center")

### Arguments

`MD` | DBAmmd Object. This Object can be created using `DBAmmd()`.
`bin.length` | size of binning window (in bp) (DEFAULT: 20)
`whichPos` | specifies which relative positions of mapped fragments should to be considered. Can be one of: 'Left.p', 'Right.p', 'Right.p' and 'Left.n': Start and end positions of fragments mapping to positive or negative strand, respectively ('Right.p' and 'Left.n' are not available for single-end reads). Additionally inferred positions: 'Center.n','Center.p','Center','Left','Right'. (DEFAULT: 'Center')

### Value

DBAmmd object with updated slot `Hists`

### See Also

`DBAmmd`, `getPeakReads`, `estimateFragmentCenters`, `plotPeak`,

### Examples

    ## Example using a small data set provided with this package:

    data("MMD")
    bin.length <- 20
    MMD.1 <- compHists(MMD,bin.length)

    # use \code{plotPeak()} to plot indivdual peaks:
    Peak.id <- '6'
    plotPeak(MMD.1, Peak.id=Peak.id)

    # or explicitly using the histograms:
    H <- Hists(MMD.1, whichPos='Center')
    Sample <- 'WT.AB2'
    Peak.idx <- match(Peak.id, names(Regions(MMD.1)))
    plot(H[[Peak.idx]][Sample,],t='l')

    # add peak cooridnates:
    Peak <- Regions(MMD.1)[Peak.idx]
    meta <- metaData(MMD.1)
    PeakBoundary <- meta$AnaData$PeakBoundary
    x.coords <- as.integer(colnames(H[[Peak.idx]])) + start(Peak) - PeakBoundary
    plot(x.coords,H[[Peak.idx]]['WT.AB2',],t='l',
        xlab=names(H)[Peak.idx], ylab='counts', main=Sample)

[Package MMDiff2 version 1.20.0 Index]