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.

clipTrk

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 = clipTrk(rawCD4[ chrnum(5), ], 1.30e8, 1.33e8 )
plot(getTrkXY(c52))