plotSSD-methods: Generate SSD plot

In ChIPQC: Quality metrics for ChIPseq data

Description

Generate SSD metric plot. If blacklists supplied, will generate SSD prior and post blacklisting

Methods

signature(object = "ChIPQCexperiment", facet=T, facetBy=c("Tissue","Factor"))

Generate SSD metric plot for all samples in experiment. If blacklists supplied, will generate SSD prior and post blacklisting

signature(object = "list", facet=T, facetBy=c("Tissue","Factor"))

Generate SSD metric plot for list of samples in experiment. If blacklists supplied, will generate SSD prior and post blacklisting

signature(object = "ChIPQCsample")

Generate SSD metric plot for single sample. If blacklists supplied, will generate SSD prior and post blacklisting

Note

plotSSD uses ggplot2 for plotting, and returns a ggplot2 plot gg object.

Author(s)

Thomas Carroll and Rory Stark

See Also

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

Examples

data(example_QCexperiment)
plotSSD(exampleExp,facetBy=c("Tissue","Factor"))
plotSSD(QCsample(exampleExp,1))
plotSSD(QCsample(exampleExp)[1:3])
data(tamoxifen_QC)
plotSSD(tamoxifen,facetBy=c("Tissue","Condition"))

ChIPQC documentation built on Nov. 8, 2020, 8:06 p.m.