XBSeqDataSet-class {XBSeq} | 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.

### See Also

`estimateSCV`, `conditions`, `dispEst`, `dispTable`, `fitInfo`, `DESeqDataSet`, `counts`, `estimateRealCount`

### Examples

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

[Package XBSeq version 1.19.0 Index]