fitInfo: Accessor function for the fitInfo objects in a XBSeqDataSet

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

Description

Same method is adopted from DESeq to access the fit information from a XBSeqDataSet

Usage

fitInfo( object, name)

Arguments

object	a XBSeqDataSet
name	if estimateSCV was called with method="per-condition" a name hasd to specified. Try ls(XB@fitInfo.

Value

A list containing fitting information for a XBSeqDataSet object:

perGeneSCVEsts	SCV estimates for each gene, which has the same length as the number of rows as the assay elements in an object
SCVFunc	The function used to predict the fitted SCV
fittedSCVEsts	The fitted SCV estimates for each gene, which is of the same length as perGeneSCVEsts
df	Integer value indicating the degree of freedom
sharingMode	The sharing mode argument specified by the user

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, XBSeqDataSet

Examples

   conditions <- factor(c(rep('C1', 3), rep('C2', 3)))
   data(ExampleData)
   XB <- XBSeqDataSet(Observed, Background, conditions)
   XB <- estimateRealCount(XB)
   XB <- estimateSizeFactors(XB)
   XB <- estimateSCV(XB, fitType='local')
   str(fitInfo(XB))

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