ucscTrackModes-methods {rtracklayer} | R Documentation

## Accessing UCSC track modes

### Description

Generics for getting and setting UCSC track visibility modes ("hide", "dense", "full", "pack", "squish").

### Methods

The following methods are defined by rtracklayer for getting the track modes through the generic `ucscTrackModes(object, ...)`.

object = "character"

  `function(object, hide = character(), dense = character(), pack = character(), squish = character(), full = character())` Creates an instance of `UCSCTrackModes` from `object`, a character vector of mode names, with the corresponding track ids given in the `names` attribute. Note that `object` can be a `UCSCTrackModes` instance, as `UCSCTrackModes` extends `character`. The other parameters are character vectors identifying the tracks for each mode and overriding the modes specified by `object`.

object = "missing"

  The same interface as above, except `object` defaults to an empty character vector.

object = "UCSCView"

  Gets modes for tracks in the view.

object = "UCSCSession"

  Gets default modes for the tracks in the session. These are the modes that will be used as the default for a newly created view.

The following methods are defined by rtracklayer for setting the track modes through the generic `ucscTrackModes(object) <- value`.

object = "UCSCView", value = "UCSCTrackModes"

  Sets the modes for the tracks in the view.

object = "UCSCView", value = "character"

  Sets the modes from a character vector of mode names, with the corresponding track names given in the `names` attribute.

### See Also

`trackNames` and `trackNames<-` for just getting or setting which tracks are visible (not of mode "hide").

### Examples

    # Tracks "foo" and "bar" are fully shown, "baz" is hidden
    modes <- ucscTrackModes(full = c("foo", "bar"), hide = "baz")
    # Update the modes to hide track "bar"
    modes2 <- ucscTrackModes(modes, hide = "bar")

[Package rtracklayer version 1.52.1 Index]