hg18track-class {encoDnaseI} | R Documentation

## Class "hg18track" container for hg18 annotation found in genome browser track files; class "chrnum" extends numeric for an indexing application on hg18track objects.

### Description

container for hg18 annotation found in genome browser track files

### Objects from the Class

Objects can be created by calls of the form `new("hg18track", assayData, featureData, experimentData, annotation, dataVals, ...)`. These are single-sample eSet instances.

Note that `demoTrk19` is a restriction of the `rawCD4` structure to the interval of chromosome 19 that was assayed in the ENCODE project for DnaseI hypersensitivity.

### Slots

`assayData`:
  Object of class `"AssayData"` ~~
`phenoData`:
  Object of class `"AnnotatedDataFrame"` ~~
`featureData`:
  Object of class `"AnnotatedDataFrame"` ~~
`experimentData`:
  Object of class `"MIAME"` ~~
`annotation`:
  Object of class `"character"` ~~
`.__classVersion__`:
  Object of class `"Versions"` ~~

### Extends

Class `"eSet"`, directly. Class `"VersionedBiobase"`, by class "eSet", distance 2. Class `"Versioned"`, by class "eSet", distance 3.

### Methods

[
  `signature(x = "hg18track")`: select using numeric, logical, or chrnum indices.
chrnum
  `signature(object = "hg18track")`: extract numeric tokens for chromosome number at which data values are obtained; note that chrnum is also used as name of a class.
dataVals
  `signature(object = "hg18track")`: actual data values
getTrkXY
  `signature(object = "hg18track", type = "character")`: obtain a list with components x, y indicating location and data value respectively; location is within chromosome; default type is 'midpoint' of locations given as intervals
getTrkXY
  `signature(object = "hg18track", type = "missing")`: take default midpoint x values corresponding to data values
rangeLocs
  `signature(object = "hg18track")`: if measures from only one chromosome are present , this returns low and high values of chromStart and chromEnd respectively, otherwise error.
clip
  `signature(obj = "hg18track", low="numeric", hi="numeric", attr="ANY")`: create a restriction of the track using an interval specification. by default the `chromStart` featureData component is used for coordinates to clip; if `attr` is non-missing, the featureData component named by `attr` will be used.
initialize
  `signature(.Object = "hg18track")`: create a new instance

### Author(s)

VJ Carey <stvjc@channing.harvard.edu>

### Examples

    showClass("hg18track")
    data(rawCD4)
    rawCD4
    rawCD4.chr1 = rawCD4[ chrnum(1), ]
    rangeLocs(rawCD4.chr1)
    plot(getTrkXY(rawCD4.chr1), ylab="data value", xlab="interval midpt on chr 1" )
    c52 = clip(rawCD4[ chrnum(5), ], 1.30e8, 1.33e8 )
    plot(getTrkXY(c52))

[Package encoDnaseI version 0.0-11 Index]