plotSCVEsts {XBSeq} | R Documentation

## 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

### 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`

### 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)

[Package XBSeq version 1.19.0 Index]