Accessors for the 'counts' slot of a DEXSeqResults 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 'DEXSeqResults'
counts(object,normalized=FALSE)

Arguments

Value

an integer matrix

Examples

  data(pasillaDEXSeqDataSet, package="pasilla")
  head( counts( dxd ))

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(DEXSeq)
Loading required package: BiocParallel
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: SummarizedExperiment
Loading required package: GenomicRanges
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: GenomeInfoDb
Loading required package: DESeq2
Loading required package: AnnotationDbi
Loading required package: RColorBrewer
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DEXSeq/counts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: counts
> ### Title: Accessors for the 'counts' slot of a DEXSeqResults object.
> ### Aliases: counts counts,DEXSeqResults-method
> 
> ### ** Examples
> 
>   data(pasillaDEXSeqDataSet, package="pasilla")
>   head( counts( dxd ))
                 [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] [,11] [,12]
FBgn0000256:E001   92   28   43   54  131   51   49 1390  829   923  1115  2495
FBgn0000256:E002  124   80   91   76  224   82   95 1358  777   875  1093  2402
FBgn0000256:E003  340  241  262  347  670  260  297 1142  616   704   822  1956
FBgn0000256:E004  250  189  201  219  507  242  250 1232  668   765   950  2119
FBgn0000256:E005   96   38   39   71   76   57   62 1386  819   927  1098  2550
FBgn0000256:E006    1    0    1    0    2    0    2 1481  857   965  1169  2624
                 [,13] [,14]
FBgn0000256:E001  1054  1052
FBgn0000256:E002  1023  1006
FBgn0000256:E003   845   804
FBgn0000256:E004   863   851
FBgn0000256:E005  1048  1039
FBgn0000256:E006  1105  1099
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>