overlapStats {csaw} | R Documentation

## Combine statistics for overlap-based clusters

### Description

Compute assorted statistics for overlaps between windows and pre-defined genomic regions in a Hits object.

### Usage

    combineOverlaps(overlaps, tab, o.weights = NULL, i.weights = NULL, ...)

    getBestOverlaps(overlaps, tab, o.weights = NULL, i.weights = NULL, ...)

    empiricalOverlaps(overlaps, tab, o.weights = NULL, i.weights = NULL, ...)

    mixedOverlaps(overlaps, tab, o.weights = NULL, i.weights = NULL, ...)

    summitOverlaps(overlaps, region.best, o.summit = NULL, i.summit = NULL)

### Arguments

`overlaps` | A Hits object produced by `findOverlaps`, containing overlaps between regions (query) and windows (subject).
`tab` | A data.frame of (differential binding) statistics for each window.
`o.weights` | A numeric vector specifying weights for each overlapped window.
`i.weights` | A numeric vector specifying weights for each individual window.
`...` | Other arguments to be passed to the wrapped functions.
`region.best` | An integer vector specifying the window index that is the summit for each region.
`o.summit` | A logical vector specifying the overlapped windows that are summits, or a corresponding integer vector of indices for such windows.
`i.summit` | A logical vector specifying whether an individual window is a summit, or a corresponding integer vector of indices.

### Details

These functions provide convenient wrappers around `combineTests`, `getBestTest`, `empiricalFDR`, `mixedClusters` and `upweightSummit` for handling overlaps between windows and arbitrary pre-specified regions. They accept Hits objects produced by running `findOverlaps` between regions (as the query) and windows (as the subject). Each set of windows overlapping a region is defined as a cluster to compute various statistics.

A wrapper is necessary as a window may overlap multiple regions. If so, the multiple instances of that window are defined as distinct “overlapped” windows, where each overlapped window is assigned to a different region. Each overlapped window is represented by a separate entry of `overlaps`. In contrast, the “individual” window just refers to the window itself, regardless of what it overlaps. This is represented by each row of the RangedSummarizedExperiment object and the `tab` derived from it.

The distinction between these two definitions is required to describe the weight arguments. The `o.weights` argument refers to the weights for each region-window relationship. This allows for different weights to be assigned to the same window in different regions. The `i.weights` argument is the weight of the window itself, and is the same regardless of the region. If both are specified, `o.weights` takes precedence.

For `summitOverlaps`, the `region.best` argument is designed to accept the `rep.test` field in the output of `getBestOverlaps` (run with `by.pval=FALSE`). This contains the index for the individual window that is the summit within each region. In contrast, the `i.summit` argument indicates whether an individual window is a summit, e.g., from `findMaxima`. The `o.summit` argument does the same for overlapped windows, though this has no obvious input within the `csaw` pipeline.

### Value

For `combineOverlaps`, `getBestOverlaps`, `empiricalOverlaps` and `mixedOverlaps`, a DataFrame is returned from their respective wrapped functions. Each row of the DataFrame corresponds to a region, where regions without overlapped windows are assigned `NA` values.

For `summitOverlaps`, a numeric vector of weights is produced. This can be used as `o.weight` in the other two functions.

### Author(s)

Aaron Lun

### See Also

`combineTests`, `getBestTest`, `empiricalFDR` and `upweightSummit`, for the underlying functions.

`findOverlaps`, to generate the required Hits object.

### Examples

    bamFiles <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
    data <- windowCounts(bamFiles, width=1, filter=1)
    of.interest <- GRanges(c('chrA', 'chrA', 'chrB', 'chrC'),
        IRanges(c(1, 500, 100, 1000), c(200, 1000, 700, 1500)))

    # Making some mock results.
    N <- nrow(data)
    mock <- data.frame(logFC=rnorm(N), PValue=runif(N), logCPM=rnorm(N))

    olap <- findOverlaps(of.interest, rowRanges(data))
    combineOverlaps(olap, mock)
    getBestOverlaps(olap, mock)
    empiricalOverlaps(olap, mock)

    # See what happens when you don't get many overlaps.
    getBestOverlaps(olap[1,], mock)
    combineOverlaps(olap[2,], mock)
    empiricalOverlaps(olap[1,], mock)

    # Weighting example, with window-specific weights.
    window.weights <- runif(N)
    comb <- combineOverlaps(olap, mock, i.weight=window.weights)
    comb <- getBestOverlaps(olap, mock, i.weight=window.weights)
    comb <- empiricalOverlaps(olap, mock, i.weight=window.weights)

    # Weighting example, with relation-specific weights.
    best.by.ave <- getBestOverlaps(olap, mock, by.pval=FALSE)
    w <- summitOverlaps(olap, region.best=best.by.ave$rep.test)
    head(w)
    stopifnot(length(w)==length(olap))
    combineOverlaps(olap, mock, o.weight=w)

    # Running summitOverlaps for window-specific summits
    # (output is still relation-specific weights, though).
    is.summit <- findMaxima(rowRanges(data), range=100, metric=mock$logCPM)
    w <- summitOverlaps(olap, i.summit=is.summit)
    head(w)

[Package csaw version 1.28.0 Index]