QCplots: Quality Control visualizations
In shiauck/cummeRbund_on_RSQLite2.0: Analysis, exploration, manipulation, and visualization of Cufflinks high-throughput sequencing data.

Description Usage Arguments Details Value Note Author(s) References Examples

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.

1 2	## S4 method for signature 'CuffData' fpkmSCVPlot(object,FPKMLowerBound=1, showPool = FALSE)

`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)

None

A ggplot2 plot object with a geom_box layer.

None

Loyal A. Goff

None

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