gridCover-class {htSeqTools} | R Documentation

## Class "gridCover"

### 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)

[Package htSeqTools version 1.28.3 Index]