XBSeq (version 1.2.2)

plotSCVEsts: Plot estimated squared coefficient of variation

Description

Plot estimated SCV based on ggplot2

Usage

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

Arguments

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

Value

Summary plot for the fitting and estimation of scv

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

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')
   plotSCVEsts(XB)