QCplots: Quality Control visualizations

In cummeRbund: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

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)

cummeRbund documentation built on Nov. 8, 2020, 7:53 p.m.