regionsCoverage: Compute coverage on user specified genomic regions.

In htSeqTools: Quality Control, Visualization and Processing for High-Throughput Sequencing data

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)

htSeqTools documentation built on May 6, 2019, 3:39 a.m.