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Last data update: 2014.03.03

R: Class '"ChIPseqSet"'

ChIPseqSet-class

R Documentation

Class `"ChIPseqSet"`

Description

A class for storing count data obtained from ChIP-seq experiments by counting the number of reads lying within regions. The class extends RangedSummarizedExperiment.

Objects from the Class

Objects can be created by calls of the form ChIPseqSet(chipVals=countDataMatrix, rowRanges=genomicRegions, colData=DataFrame(row.names=colnames(countDataMatrix)), ...). However, one will most likely create a ChIPseqSet object by calling summarizeReads.

Slots

metadata:: An optional list of arbitrary content describing the overall experiment.
rowRanges:: Object of class "GRanges" or "GRangesList" containing the genomic regions where the reads were counted.
colData:: Object of class "DataFrame" containing information on variable values of the samples. Some methods require the total library size of each sample stored in a column titled totalCounts.
assays:: Object of class SimpleList of a matrix, named chipVals containing the read counts per genomic region.

Extends

Class "RangedSummarizedExperiment", directly.

Methods

chipVals: signature(object = "ChIPseqSet"): Returns the matrix with read counts.
chipVals<-: signature(object = "ChIPseqSet", value = "matrix"): Sets the matrix with read counts.
cpm: signature(object = "ChIPseqSet", libSize, log2=FALSE, priorCount=0.1): Returns an object of ChIPseqSet with read counts standardized by library size - counts per million (cpm). If the library size is not given, the column sums of the given object are used. Cpm values are logarithmized after adding priorCounts, if log2 is TRUE.

Author(s)

Hans-Ulrich Klein (hklein@broadinstitute.org)

Examples

showClass("ChIPseqSet")

Results


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> library(epigenomix)
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/epigenomix/ChIPseqSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ChIPseqSet-class
> ### Title: Class '"ChIPseqSet"'
> ### Aliases: ChIPseqSet-class ChIPseqSet ChIPseqSet,matrix,GRanges-method
> ###   ChIPseqSet,matrix,GRangesList-method chipVals<-
> ###   chipVals<-,ChIPseqSet,matrix-method chipVals
> ###   chipVals,ChIPseqSet-method cpm cpm,ChIPseqSet-method
> ### Keywords: classes
> 
> ### ** Examples
> 
> showClass("ChIPseqSet")
Class "ChIPseqSet" [package "epigenomix"]

Slots:
                                                            
Name:                   rowRanges                    colData
Class: GenomicRangesORGRangesList                  DataFrame
                                                            
Name:                      assays                      NAMES
Class:                     Assays            characterORNULL
                                                            
Name:             elementMetadata                   metadata
Class:                  DataFrame                       list

Extends: 
Class "RangedSummarizedExperiment", directly
Class "SummarizedExperiment", by class "RangedSummarizedExperiment", distance 2
Class "Vector", by class "RangedSummarizedExperiment", distance 3
Class "Annotated", by class "RangedSummarizedExperiment", distance 4
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

Class "ChIPseqSet"