ChIPQCreport: Generate a summary QC report

In shengqh/ChIPQC: Quality metrics for ChIPseq data

Generate a summary QC report

Description

Generate an HTML summary QC report.

Methods

signature(experiment = "ChIPQCexperiment", facet=TRUE, reportName="ChIPQC", reportFolder="ChIPQCreport", facetBy=c("Tissue","Factor","Condition","Treatment"), colourBy=c("Replicate"))

Generates an summary QC report for the experiment in HTML format.

experiment	ChIPQCexperiment object
facet	logical indicating whether or not to facet using experimental metadata.
reportName	filename of main report file (.html).
reportFolder	directory name where plot graphics will be saved
facetBy	metadata fields to use for faceting
colourBy	metadata field to color by

signature(experiment = "list", facet=TRUE, reportName="ChIPQC", reportFolder="ChIPQCreport", facetBy=c("Sample"), colourBy=c("Sample"))

Generates an summary QC report for a list of ChIPQCsample objects in HTML format.

experiment	list object
facet	logical indicating whether or not to facet using experimental metadata.
reportName	filename of main report file (.html).
reportFolder	directory name where plot graphics will be saved
facetBy	metadata fields to use for faceting
colourBy	metadata field to color by

signature(sample = "ChIPQCsample", reportName="ChIPQC", reportFolder="ChIPQCreport",)

Generate a summary QC report for a sample in HTML format.

sample	ChIPQCsample object
reportName	filename of main report file (.html).
reportFolder	directory name where plot graphics will be saved

Note

ChIPQCreport uses Nozzle.R2 for generating HTML.

Author(s)

Thomas Carroll and Rory Stark

See Also

ChIPQC-package, ChIPQCexperiment, ChIPQCsample

Examples

data(example_QCexperiment)
ChIPQCreport(exampleExp,facetBy=c("Tissue","Factor"))
#report in ChIPQCreport/Example.html

data(tamoxifen_QC)
ChIPQCreport(tamoxifen,facetBy="Tissue",colourBy="Condition")
#report in ChIPQCreport/ChIPQC.html

ChIPQCreport(tamoxifen,facetBy=c("Tissue","Condition"))
#report in ChIPQCreport/ChIPQC.html

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