Accessor function for the fitInfo objects in a XBSeqDataSet

Description

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

Usage

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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

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   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))