XBSeqDataSet-class: Class '"XBSeqDataSet"'

In XBSeq: Test for differential expression for RNA-seq data

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)

XBSeq documentation built on Nov. 8, 2020, 11:12 p.m.