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Last data update: 2014.03.03

R: Class '"XBSeqDataSet"'

XBSeqDataSet-class

R Documentation

Class `"XBSeqDataSet"`

Description

XBSeqDataSet is a subclass of "DESeqDataSet", used to store the input values, intermediate calculations and results of an analysis of differential expression. Different from the original DESeqDataSet class, XBSeqDataSet has some extra slots including:

fitInfo: An object of environment class which contains the scv fitting information for a XBSeqDataSet object
dispTable: An object of character class which indicates method used for scv fitting. Details can be found in estimateSCV.
conditions: An object of factor class which contains the experimental design information for a XBSeqDataSet object
dispEst: An object of list class which contains the final dispersion estimates for each gene. Details can be found in dispEst

Usage

XBSeqDataSet(counts, bgcounts, conditions, sizeFactors=NULL, ...)

Arguments

`counts`	A data frame or matrix which contains the observed signal for each gene across all the samples. Rows represent genes and columns represent samples.
`bgcounts`	A data frame or matrix which contains the background noise for each gene across all the samples. Rows represent genes and columns represent samples.
`conditions`	Object of class `"character"`. The conditions for the experimental design.
`sizeFactors`	Numeric vector which contains normalizing factors for the data matrix. In most cases, it is recommended that you calculate sizeFactors by `estimateSizeFactors`. You are also able to provide sizeFactors yourself.
`...`	Further arguments provided will be ignored

Value

A XBSeqDataSet object.

Methods

conditions: signature(object = "XBSeqDataSet"): ...
conditions<-: signature(object = "XBSeqDataSet"): ...
counts: signature(object = "XBSeqDataSet"): ...
dispTable: signature(object = "XBSeqDataSet"): ...
dispEst: signature(object = "XBSeqDataSet"): ...
dispEst<-: signature(object = "XBSeqDataSet"): ...
fitInfo: signature(object = "XBSeqDataSet"): ...
fitInfo<-: signature(object = "XBSeqDataSet"): ...
estimateSCV: signature(object = "XBSeqDataSet"): ...
estimateSizeFactors: signature(object = "XBSeqDataSet"): ...
estimateRealCount: signature(object = "XBSeqDataSet"): ...

Author(s)

Yuanhang Liu

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.

Examples

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

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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
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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/XBSeqDataSet-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: XBSeqDataSet-class
> ### Title: Class '"XBSeqDataSet"'
> ### Aliases: XBSeqDataSet-class XBSeqDataSet
> 
> ### ** Examples
> 
>    data(ExampleData)
>    conditions <- factor(c(rep('C1', 3), rep('C2', 3)))
>    XB <- XBSeqDataSet(Observed, Background, conditions)
>    str(XB)
Formal class 'XBSeqDataSet' [package "XBSeq"] with 12 slots
  ..@ fitInfo           :<environment: 0xfd90ee0> 
  ..@ dispTable         : chr [1:2] NA NA
  ..@ conditions        : Factor w/ 2 levels "C1","C2": 1 1 1 2 2 2
  ..@ dispEst           : list()
  ..@ design            :Class 'formula'  language ~conditions
  .. .. ..- attr(*, ".Environment")=<environment: 0xf6a9c58> 
  ..@ dispersionFunction:function ()  
  ..@ rowRanges         :Formal class 'GRangesList' [package "GenomicRanges"] with 5 slots
  .. .. ..@ unlistData     :Formal class 'GRanges' [package "GenomicRanges"] with 6 slots
  .. .. .. .. ..@ seqnames       :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. .. .. .. .. ..@ values         : Factor w/ 0 levels: 
  .. .. .. .. .. .. ..@ lengths        : int(0) 
  .. .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. .. ..@ metadata       : list()
  .. .. .. .. ..@ ranges         :Formal class 'IRanges' [package "IRanges"] with 6 slots
  .. .. .. .. .. .. ..@ start          : int(0) 
  .. .. .. .. .. .. ..@ width          : int(0) 
  .. .. .. .. .. .. ..@ NAMES          : NULL
  .. .. .. .. .. .. ..@ elementType    : chr "integer"
  .. .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. .. ..@ metadata       : list()
  .. .. .. .. ..@ strand         :Formal class 'Rle' [package "S4Vectors"] with 4 slots
  .. .. .. .. .. .. ..@ values         : Factor w/ 3 levels "+","-","*": 
  .. .. .. .. .. .. ..@ lengths        : int(0) 
  .. .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. .. ..@ metadata       : list()
  .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. .. .. .. .. ..@ rownames       : NULL
  .. .. .. .. .. .. ..@ nrows          : int 0
  .. .. .. .. .. .. ..@ listData       : Named list()
  .. .. .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. .. ..@ metadata       : list()
  .. .. .. .. ..@ seqinfo        :Formal class 'Seqinfo' [package "GenomeInfoDb"] with 4 slots
  .. .. .. .. .. .. ..@ seqnames   : chr(0) 
  .. .. .. .. .. .. ..@ seqlengths : int(0) 
  .. .. .. .. .. .. ..@ is_circular: logi(0) 
  .. .. .. .. .. .. ..@ genome     : chr(0) 
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. .. .. ..@ rownames       : NULL
  .. .. .. .. ..@ nrows          : int 22609
  .. .. .. .. ..@ listData       : Named list()
  .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. .. .. .. .. ..@ rownames       : NULL
  .. .. .. .. .. .. ..@ nrows          : int 0
  .. .. .. .. .. .. ..@ listData       :List of 2
  .. .. .. .. .. .. .. ..$ type       : chr(0) 
  .. .. .. .. .. .. .. ..$ description: chr(0) 
  .. .. .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. .. ..@ metadata       : list()
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ partitioning   :Formal class 'PartitioningByEnd' [package "IRanges"] with 5 slots
  .. .. .. .. ..@ end            : int [1:22609] 0 0 0 0 0 0 0 0 0 0 ...
  .. .. .. .. ..@ NAMES          : chr [1:22609] "0610005C13Rik" "0610007C21Rik" "0610007L01Rik" "0610007P08Rik" ...
  .. .. .. .. ..@ elementType    : chr "integer"
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ elementType    : chr "GRanges"
  .. .. ..@ metadata       : list()
  ..@ colData           :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. ..@ rownames       : chr [1:6] "Sample_54_WT" "Sample_72_WT" "Sample_93_WT" "Sample_31_MYC" ...
  .. .. ..@ nrows          : int 6
  .. .. ..@ listData       :List of 1
  .. .. .. ..$ conditions: Factor w/ 2 levels "C1","C2": 1 1 1 2 2 2
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata:Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. .. .. ..@ rownames       : NULL
  .. .. .. .. ..@ nrows          : int 1
  .. .. .. .. ..@ listData       :List of 2
  .. .. .. .. .. ..$ type       : chr "input"
  .. .. .. .. .. ..$ description: chr ""
  .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. ..@ metadata       : list()
  .. .. ..@ metadata       : list()
  ..@ assays            :Reference class 'ShallowSimpleListAssays' [package "SummarizedExperiment"] with 1 field
  .. ..$ data: NULL
  .. ..and 14 methods.
  ..@ NAMES             : NULL
  ..@ elementMetadata   :Formal class 'DataFrame' [package "S4Vectors"] with 6 slots
  .. .. ..@ rownames       : NULL
  .. .. ..@ nrows          : int 22609
  .. .. ..@ listData       : Named list()
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
  ..@ metadata          :List of 1
  .. ..$ version:Classes 'package_version', 'numeric_version'  hidden list of 1
  .. .. ..$ : int [1:3] 1 12 3
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>

Class "XBSeqDataSet"