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

Description

The 'counts' function extract a certian assay element from XBSeqDataSet object. The normalized assay element can be extracted by specifying 'normalized = TRUE'.

Usage

## S4 method for signature 'XBSeqDataSet'
counts(object,slot = 3, normalized = FALSE)

Arguments

Details

counts is a function to access an array elemen which is specified by the end user. The difference between this function and the counts function for DESeqDataSet is that this function can be used to access a specific array elememt rather than a pre-defined array element "counts" in the case of DESeqDataSet. By default, the first array element contains information of observed signal. The second array element contains information of background noise. The third array element contains information of estimated true signal after calling the function estimateRealCount.

Value

Either normalized or un-normalized assay element

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, DESeqDataSet

Examples

   data(ExampleData)
   conditions <- factor(c(rep('C1', 3), rep('C2', 3)))
   XB <- XBSeqDataSet(Observed, Background, conditions)
   str(counts(XB, 1))

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/counts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: counts
> ### Title: Accessor functions for the 'counts' information in a
> ###   XBSeqDataSet object.
> ### Aliases: counts counts,XBSeqDataSet-method
> 
> ### ** Examples
> 
>    data(ExampleData)
>    conditions <- factor(c(rep('C1', 3), rep('C2', 3)))
>    XB <- XBSeqDataSet(Observed, Background, conditions)
>    str(counts(XB, 1))
 int [1:22609, 1:6] 3683 2136 2826 717 3138 298 115 0 759 961 ...
 - attr(*, "dimnames")=List of 2
  ..$ : chr [1:22609] "0610005C13Rik" "0610007C21Rik" "0610007L01Rik" "0610007P08Rik" ...
  ..$ : chr [1:6] "Sample_54_WT" "Sample_72_WT" "Sample_93_WT" "Sample_31_MYC" ...
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>