track-class {trackViewer} | R Documentation

## Class `"track"`

### Description

An object of class `"track"` represents scores of a given track.

### Usage

        ## S4 method for signature 'track,character,ANY'
    setTrackStyleParam(ts, attr, value)
        ## S4 method for signature 'track,character,ANY'
    setTrackXscaleParam(ts, attr, value)
        ## S4 method for signature 'track,character,ANY'
    setTrackYaxisParam(ts, attr, value)

### Arguments

`ts` | An object of `track`.
`attr` | the name of slot of `trackStyle` object to be changed.
`value` | values to be assigned.

### Objects from the Class

Objects can be created by calls of the form `new("track", dat, dat2, type, format, style, name)`.

### Slots

`dat`

  Object of class `GRanges` the scores of a given track. It should contain score metadata.

`dat2`

  Object of class `GRanges` the scores of a given track. It should contain score metadata. When dat2 and dat is paired, dat will be drawn as positive value where dat2 will be drawn as negative value (-1 * score)

`type`

  The type of track. It could be 'data' or 'gene'.

`format`

  The format of the input. It could be "BED", "bedGraph", "WIG", "BigWig" or "BAM"

`style`

  Object of class `trackStyle`

`name`

  unused yet

### Methods

setTrackStyleParam

  change the slot values of `trackStyle` object for an object of `track`

setTrackXscaleParam

  change the `xscale` slot values for an object of `track`

setTrackYaxisParam

  change the `yaxisStyle` values for an object of `track`

$, $<-

  Get or set the slot of `track`

show

  show the detials of `track`

### See Also

Please try to use `importScore` and `importBam` to generate the object.

### Examples

        extdata <- system.file("extdata", package="trackViewer",
                           mustWork=TRUE)
        fox2 <- importScore(file.path(extdata, "fox2.bed"), format="BED")
        setTrackStyleParam(fox2, "color", c("red","green"))
        setTrackXscaleParam(fox2, "gp", list(cex=.5))
        setTrackYaxisParam(fox2, "gp", list(col="blue"))
        fox2$dat <- GRanges(score=numeric(0))

[Package trackViewer version 1.14.1 Index]