plotSSD-methods: Generate SSD plot

In shengqh/ChIPQC: Quality metrics for ChIPseq data

Generate SSD plot

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"))

shengqh/ChIPQC documentation built on Feb. 27, 2023, 10:51 p.m.