Accessors for the 'DESeq2Data' slot of a DChIPRepResults object.

Description

The slot contains the DESeqDataSet as it is obtained after the initial data import. The DESeqDataSet contains the counts per position and the normalization factors as computed using the input counts.

Usage

## S4 method for signature 'DChIPRepResults'
DESeq2Data(object)

## S4 replacement method for signature 'DChIPRepResults,DESeqDataSet'
DESeq2Data(object) <- value

Arguments

Value

the DESeq2Data object contained in the DChIPRepResults object

Examples

data(testData)
dcr <- DChIPRepResults(testData)
DESeq2Data(dcr)

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(DChIPRep)
Loading required package: DESeq2
Loading required package: S4Vectors
Loading required package: stats4
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


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
Loading required package: Biobase
Welcome to Bioconductor

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


Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi' 
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DChIPRep/DESeq2Data.Rd_%03d_medium.png", width=480, height=480)
> ### Name: DESeq2Data
> ### Title: Accessors for the 'DESeq2Data' slot of a 'DChIPRepResults'
> ###   object.
> ### Aliases: DESeq2Data DESeq2Data,DChIPRepResults-method DESeq2Data<-
> ###   DESeq2Data<-,DChIPRepResults,DESeqDataSet-method
> 
> ### ** Examples
> 
> data(testData)
> dcr <- DChIPRepResults(testData)
> DESeq2Data(dcr)
class: DESeqDataSet 
dim: 2500 6 
metadata(0):
assays(2): counts normalizationFactors
rownames(2500): Pos_-1000 Pos_-999 ... Pos_1498 Pos_1499
rowData names(0):
colnames(6): 1 2 ... 5 6
colData names(6): ChIP Input ... condition sampleID
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>