htSeqTools (version 1.18.0)

regionsCoverage: 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

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)