ChIPQCexperiment-class: ChIPQCexperiment instances

ChIPQCexperiment-classR 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 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

genialis/ChIPQC documentation built on May 24, 2022, 5:24 p.m.