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))

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(encoDnaseI)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: lattice
Loading required package: GGtools
Loading required package: GGBase
Loading required package: snpStats
Loading required package: survival
Loading required package: Matrix
Loading required package: data.table
Loading required package: Homo.sapiens
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:Matrix':

    colMeans, colSums, expand, rowMeans, rowSums

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums


Attaching package: 'IRanges'

The following object is masked from 'package:data.table':

    shift

Loading required package: OrganismDbi
Loading required package: GenomicFeatures
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: GO.db

Loading required package: org.Hs.eg.db

Loading required package: TxDb.Hsapiens.UCSC.hg19.knownGene

Attaching package: 'GGtools'

The following object is masked from 'package:stats':

    getCall

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/encoDnaseI/hg18track-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: hg18track-class
> ### Title: Class "hg18track" container for hg18 annotation found in genome
> ###   browser track files; class "chrnum" extends numeric for an indexing
> ###   application on hg18track objects.
> ### Aliases: hg18track-class chrnum-class [,hg18track-method
> ###   chrnum,numeric-method chrnum,hg18track-method chrnum rangeLocs
> ###   chromStarts chromStarts,hg18track-method dataVals,hg18track-method
> ###   rangeLocs,hg18track-method getTrkXY dataVals
> ###   getTrkXY,hg18track,character-method getTrkXY,hg18track,missing-method
> ###   initialize,hg18track-method demoTrk19 clipTrk
> ###   clipTrk,hg18track,numeric,numeric,ANY-method
> ###   clipTrk,hg18track,numeric,numeric-method
> ###   [,hg18track,ANY,ANY,ANY-method makeHg18track
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("hg18track")
Class "hg18track" [package "encoDnaseI"]

Slots:
                                                               
Name:           assayData          phenoData        featureData
Class:          AssayData AnnotatedDataFrame AnnotatedDataFrame
                                                               
Name:      experimentData         annotation       protocolData
Class:              MIAxE          character AnnotatedDataFrame
                         
Name:   .__classVersion__
Class:           Versions

Extends: 
Class "eSet", directly
Class "VersionedBiobase", by class "eSet", distance 2
Class "Versioned", by class "eSet", distance 3
> data(rawCD4)
> rawCD4
hg18track (storageMode: lockedEnvironment)
assayData: 382713 features, 1 samples 
  element names: dataVals 
protocolData: none
phenoData: none
featureData
  featureNames: 1 2 ... 382713 (382713 total)
  fvarLabels: bin chrom chromStart chromEnd
  fvarMetadata: labelDescription
experimentData: use 'experimentData(object)'
  pubMedIds: 16791207 
Annotation:  
> rawCD4.chr1 = rawCD4[ chrnum(1), ]
Found more than one class "chrnum" in cache; using the first, from namespace 'GGBase'
Found more than one class "chrnum" in cache; using the first, from namespace 'GGBase'
> rangeLocs(rawCD4.chr1)
[1] 149424685 149924472
> plot(getTrkXY(rawCD4.chr1), ylab="data value", xlab="interval midpt on chr 1" )
> c52 = clipTrk(rawCD4[ chrnum(5), ], 1.30e8, 1.33e8 )
Found more than one class "chrnum" in cache; using the first, from namespace 'GGBase'
> plot(getTrkXY(c52))
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>