ChIPQCreport: Generate a summary QC report

ChIPQCreport-methodsR Documentation

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.