plotSCVEsts: Plot estimated squared coefficient of variation
In XBSeq: Test for differential expression for RNA-seq data

Description Usage Arguments Value Author(s) References See Also Examples

Plot estimated SCV based on ggplot2

1 2	plotSCVEsts(XB, name = NULL, ymin, linecol = "red3", xlab = "mean of normalized counts", ylab = "SCV")

`XB`	A XBSeqDataSet object
`name`	The name of the fit information. Only specify this if you choose `method="per-condition"`
`ymin`	The limit of y axis
`linecol`	The linecolour of the SCV-mean trend
`xlab`	The lable of x axis
`ylab`	The lable of y axis

Summary plot for the fitting and estimation of scv

Yuanhang Liu

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.

estimateSCV

   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')
   plotSCVEsts(XB)