Accessor functions for the 'conditions' information in a CountDataSet object.

Description

The conditions vector is a factor that assigns to each column of the count data a condition (or treatment, or phenotype, or the like). This information is stored in the CountDataSet's "phenoData" slot as a row named "condition".

Usage

## S4 method for signature 'CountDataSet'
conditions(object, ...)
## S4 replacement method for signature 'CountDataSet'
conditions(object) <- value

Arguments

Author(s)

Simon Anders, sanders@fs.tum.de

Examples

   cds <- makeExampleCountDataSet()
   conditions( cds )

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(DESeq)
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

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")'.

Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance, usability and
    functionality, please consider migrating to 'DESeq2'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/DESeq/conditions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: conditions
> ### Title: Accessor functions for the 'conditions' information in a
> ###   CountDataSet object.
> ### Aliases: conditions,CountDataSet-method
> ###   conditions<-,CountDataSet-method conditions
> 
> ### ** Examples
> 
>    cds <- makeExampleCountDataSet()
>    conditions( cds )
A1 A2 B1 B2 B3 
 A  A  B  B  B 
Levels: A B
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>