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 ofUCSCTrackModes
fromobject
, a character vector of mode names, with the corresponding track ids given in thenames
attribute. Note thatobject
can be aUCSCTrackModes
instance, asUCSCTrackModes
extendscharacter
. The other parameters are character vectors identifying the tracks for each mode and overriding the modes specified byobject
. - 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")