gridCover-class: Class "gridCover"

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

Description

Objects of class gridCover store coverage information evaluated on a grid on pre-specified genomic regions.

Objects from the Class

Objects of this class are returned by call to the function gridCoverage.

Slots

cover:

Object of class "matrix" with one row for each genomic region of interest, and 500 columns. Columns 1-100 contain the coverage in the promoter region (as specified in argument promoterDistance to gridCoverage). Columns 101-500 contain the coverage between start and end as indicated to promoterDistance.

viewsInfo:

Object of class "DataFrame" with information relative to each region (strand, mean and maximum coverage).

Methods

plot

signature(x = "gridCover", y = "ANY"): Plot the coverage.

lines

signature(x = "gridCover"): Add lines to an existing plot.

show

signature(object = "gridCover"): Show method.

stdGrid

signature(x = "gridCover"): Standardize the coverage by dividing by either the mean or the maximum coverage in each region.

getViewsinfo

signature(x = "gridCover"): Accessor for the viewsInfo slot.

getCover

signature(x = "gridCover"): Accessor for the cover slot.

Author(s)

David Rossell

See Also

regionsCoverage to compute coverage on pre-specified regions, gridCoverage to compute coverage on a grid.

Examples

##See help(gridCoverage)

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