regionsCoverage {htSeqTools} | R Documentation

## Compute coverage on user specified genomic regions.

### Description

`regionsCoverage` computes coverage for user specified genomic regions.

`gridCoverage` evaluates the coverage on a regular grid with the same number of points for each region (facilitating further plotting, clustering etc).

`stdGrid` standardized the coverage by diviging by the average or maximum coverage at each region.

### Usage

    regionsCoverage(chr, start, end, cover)

    gridCoverage(cover)

    stdGrid(cover, colname="maxCov")

### Arguments

`chr` | Vector with chromosome names.
`start` | Vector with start position. `start>end` indicates that region is on the negative strand.
`end` | Vector with end position. `start>end` indicates that region is on the negative strand.
`cover` | For `regionsCoverage`, `cover` is an object of class `RleList` with the genome-wide coverage (typically obtained by a previous call to `coverage`). For `gridCoverage` this is the coverage evaluated at user-specified regions, as returned by `regionsCoverage`. For `stdGrid` this is the coverage evaluated on a grid, as returned by `gridCoverage`.
`colname` | Name of the column in `cover@viewsInfo` to be used for the standardizing. Currently only `"meanCov"` and `"maxCov"` are implemented.

### Value

`regionsCoverage` returns a list with two components

`views` | `RleViewsList` with coverage evaluated at specified regions. Orientation is always so that start<end, i.e. For most practical purposes, regions on the reverse strand will need to be inverted.
`viewsInfo` | `SplitDataFrameList` containing information about each peak (chromosome, strand, mean and maximum coverage).

`gridCoverage` and `stdGrid` return an object of class `gridCover`. The slot `cover` is a matrix with the coverage evaluated on a grid of 500 equi-spaced points, whereas the slot `viewsInfo` is the same as that returned by `regionsCoverage` (see above). For regions between 100bp and 500bp long, a linear interpolation is used to evaluate the coverage on the 500 points grid. For regions less than 100bp long, NAs are returned.

### Methods

Methods for `regionsCoverage`:

`signature(chr = "ANY", start = "ANY", end = "ANY", cover = "RleList")`

  Evaluates the coverage `cover` at the genomic positions specified by `chr`, `start`, `end`.

Methods for `stdGrid`:

`signature(cover = "gridCover")`

  Standardizes the coverage evaluated on a grid (typically, as returned by `gridCoverage`) by dividing by the mean or maximum coverage.

### See Also

`gridCover-class`

### Examples

    #See help(enrichedPeaks)

[Package htSeqTools version 1.28.3 Index]