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