ChIPQCexperiment-class: ChIPQCexperiment instances
In shengqh/ChIPQC: Quality metrics for ChIPseq data

ChIPQCexperiment-class

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

Examples

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

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

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