QCplots {cummeRbund} | R Documentation

## Quality Control visualizations

### Description

A collection of ggplot2 visualizations for quality control assessment of cuffdiff output.

- fpkmSCVPlot: A measure of cross-replicate variability, the squared coefficient of variation is a normalized measure of variance between empirical repicate FPKM values per condition, across the range of FPKM estimates.

### Usage

    ## S4 method for signature 'CuffData'
    fpkmSCVPlot(object,FPKMLowerBound=1, showPool = FALSE)

### Arguments

`object` | An object of class CuffData.
`FPKMLowerBound` | A lower limit cutoff for FPKM values from which a fit of squared Coefficient of variation (default: 1)
`showPool` | Logical argument whether to display variability across all replicates independent of condition (TRUE) or the cross-replicate variability for each condition (FALSE)

### Details

None

### Value

A ggplot2 plot object with a geom_box layer.

### Note

None

### Author(s)

Loyal A. Goff

### References

None

### Examples

    	a<-readCufflinks(system.file("extdata", package="cummeRbund")) #Read cufflinks data and create CuffSet object
    	genes<-a@genes #CuffData object for all genes
    	csBoxplot(genes)

[Package cummeRbund version 2.36.0 Index]