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

Description

Conditions extract the experimental design information similar as used in DESeq.

Usage

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

Arguments

Value

The experimental design information for a XBSeqDataSet object

References

H. I. Chen, Y. Liu, Y. Zou, Z. Lai, D. Sarkar, Y. Huang, et al., "Differential expression analysis of RNA sequencing data by incorporating non-exonic mapped reads," BMC Genomics, vol. 16 Suppl 7, p. S14, Jun 11 2015.

See Also

XBSeqDataSet

Examples

   data(ExampleData)
   conditions <- factor(c(rep('C1', 3), rep('C2', 3)))
   XB <- XBSeqDataSet(Observed, Background, conditions)
   conditions(XB)

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(XBSeq)
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")'.

    Welcome to 'XBSeq'.
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/XBSeq/conditions.Rd_%03d_medium.png", width=480, height=480)
> ### Name: conditions
> ### Title: Accessor functions for the 'conditions' information in a
> ###   XBSeqDataSet object.
> ### Aliases: conditions conditions<-,XBSeqDataSet-method
> ###   conditions,XBSeqDataSet-method
> 
> ### ** Examples
> 
>    data(ExampleData)
>    conditions <- factor(c(rep('C1', 3), rep('C2', 3)))
>    XB <- XBSeqDataSet(Observed, Background, conditions)
>    conditions(XB)
 Sample_54_WT  Sample_72_WT  Sample_93_WT Sample_31_MYC Sample_75_MYC 
           C1            C1            C1            C2            C2 
Sample_87_MYC 
           C2 
Levels: C1 C2
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>