ChIPQCexperiment-class {ChIPQC} | R Documentation

## ChIPQCexperiment instances

### Description

The `ChIPQCexperiment` class is built around a list of `ChIPQCsample` objects, each representing a ChIP or control sample in a ChIP-seq experiment. These objects are created using the `ChIPQC` function.

### Slots

`.Data`:

  Object of class `"list"`: internal

`Samples`:

  Object of class `"list"`: List of `ChIPQCsample` objects.

`DBA`:

  Object of class `"DBA"`: `DBA` object (from package `DiffBind`)

`annotation`:

  Object of class `"list"` : annotation data

### Extends

Class `"list"`.

### Methods

QCmetadata

  `signature(object = "ChIPQCexperiment")`: see `QCmetadata`.

QCmetrics

  `signature(object = "ChIPQCexperiment")`: see `QCmetrics`.

QCsample

  `signature(object = "ChIPQCexperiment")`: see `QCsample`.

QCcontrol

  `signature(object = "ChIPQCexperiment")`: see `QCcontrol`.

QCannotation

  `signature(object = "ChIPQCexperiment")`: see `QCannotation`.

QCdba

  `signature(object = "ChIPQCexperiment")`: see `QCdba`.

averagepeaksignal

  `signature(object = "ChIPQCexperiment")`: see `averagepeaksignal`.

coveragehistogram

  `signature(object = "ChIPQCexperiment")`: see `coveragehistogram`.

crosscoverage

  `signature(object = "ChIPQCexperiment")`: see `crosscoverage`.

flagtagcounts

  `signature(object = "ChIPQCexperiment")`: see `flagtagcounts`.

fragmentlength

  `signature(object = "ChIPQCexperiment")`: see `fragmentlength`.

FragmentLengthCrossCoverage

  `signature(object = "ChIPQCexperiment")`: see `FragmentLengthCrossCoverage`.

frip

  `signature(object = "ChIPQCexperiment")`: see `frip`.

mapped

  `signature(object = "ChIPQCexperiment")`: see `mapped`.

reads

  `signature(object = "ChIPQCexperiment")`: see `reads`.

duplicates

  `signature(object = "ChIPQCexperiment")`: see `duplicates`.

duplicateRate

  `signature(object = "ChIPQCexperiment")`: see `duplicateRate`.

Normalisedaveragepeaksignal

  `signature(object = "ChIPQCexperiment")`: see `Normalisedaveragepeaksignal`.

peaks

  `signature(object = "ChIPQCexperiment")`:see `peaks`.

readlength

  `signature(object = "ChIPQCexperiment")`: see `readlength`.

ReadLengthCrossCoverage

  `signature(object = "ChIPQCexperiment")`: see `ReadLengthCrossCoverage`.

RelativeCrossCoverage

  `signature(object = "ChIPQCexperiment")`:see `RelativeCrossCoverage`.

ribl

  `signature(object = "ChIPQCexperiment")`: see `ribl`.

rip

  `signature(object = "ChIPQCexperiment")`: see `rip`.

show

  `signature(object = "ChIPQCexperiment")`: see `show`.

ssd

  `signature(object = "ChIPQCexperiment")`: see `ssd`.

regi

  `signature(object = "ChIPQCexperiment")`: see `regi`.

plotCC

  `signature(object = "ChIPQCexperiment")`: see `plotCC`.

plotCoverageHist

  `signature(object = "ChIPQCexperiment")`: see `plotCoverageHist`.

plotFribl

  `signature(object = "ChIPQCexperiment")`: see `plotFribl`.

plotPeakProfile

  `signature(object = "ChIPQCexperiment")`: see `plotPeakProfile`.

plotRap

  `signature(object = "ChIPQCexperiment")`: see `plotRap`.

plotRegi

  `signature(object = "ChIPQCexperiment")`: see `plotRegi`.

plotCorHeatmap

  `signature(object = "ChIPQCexperiment")`: see `plotCorHeatmap`.

plotPrincomp

  `signature(object = "ChIPQCexperiment")`: see `plotPrincomp`.

ChIPQCreport

  `signature(object = "ChIPQCexperiment")`: see `ChIPQCreport`.

### Author(s)

Thomas Carroll and Rory Stark

### See Also

ChIPQC-package, ChIPQCsample, DiffBind

### Examples

    ## Not run: exampleExp = ChIPQC(samples)
    data(example_QCexperiment)
    exampleExp

    ## Not run: tamoxifen = ChIPQC(samples, consensus=TRUE, bCounts=T)
    data(tamoxifen_QC)
    tamoxifen

[Package ChIPQC version 1.22.0 Index]