Accessors for the 'counts' slot of a DESeqDataSet object.

Description

The counts slot holds the count data as a matrix of non-negative integer count values, one row for each observational unit (gene or the like), and one column for each sample.

Usage

## S4 method for signature 'DESeqDataSet'
counts(object, normalized = FALSE,
  replaced = FALSE)

## S4 replacement method for signature 'DESeqDataSet,matrix'
counts(object) <- value

Arguments

Author(s)

Simon Anders

See Also

sizeFactors, normalizationFactors

Examples

dds <- makeExampleDESeqDataSet(m=4)
head(counts(dds))

dds <- estimateSizeFactors(dds) # run this or DESeq() first
head(counts(dds, normalized=TRUE))

Results

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> library(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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DESeq2/counts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: counts
> ### Title: Accessors for the 'counts' slot of a DESeqDataSet object.
> ### Aliases: counts counts,DESeqDataSet-method
> ###   counts<-,DESeqDataSet,matrix-method
> 
> ### ** Examples
> 
> 
> dds <- makeExampleDESeqDataSet(m=4)
> head(counts(dds))
      sample1 sample2 sample3 sample4
gene1      61     110      34      88
gene2       8      18      13       9
gene3      23      32      27       8
gene4       6       1       1       2
gene5       1       0       9       2
gene6      30       0      12       4
> 
> dds <- estimateSizeFactors(dds) # run this or DESeq() first
> head(counts(dds, normalized=TRUE))
         sample1     sample2    sample3   sample4
gene1 59.9058084 106.2842100 33.9103838 87.421140
gene2  7.8564995  17.3919616 12.9657350  8.940798
gene3 22.5874359  30.9190429 26.9288342  7.947376
gene4  5.8923746   0.9662201  0.9973642  1.986844
gene5  0.9820624   0.0000000  8.9762781  1.986844
gene6 29.4618730   0.0000000 11.9683707  3.973688
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>