ChIPQCreport-methods {ChIPQC} | R 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

[Package ChIPQC version 1.28.0 Index]