ChIPQCsample-class: Class '"ChIPQCsample"'

In shengqh/ChIPQC: Quality metrics for ChIPseq data

Class "ChIPQCsample"

Description

Object containing quality metrics computed for a ChIP-seq (or associated control) sample.

Objects from the Class

Objects can be created using the ChIPQCsample function.

Constructor Function

ChIPQCsample(reads, peaks, annotation, chromosomes = NULL, mapQCth = 15, blacklist, profileWin = 400, fragmentLength = 125, shifts = 1:300, runCrossCor = FALSE,verboseT=FALSE)

• readscharacter string filename of .bam file

• peaksGRanges object or character string filename of peaks. If present, peak-based metrics will be computed.

• annotation Either a character string indicating the genome and version to use as a genomic annotation, or a previously defined annotation (obtained using QCannotation on a previously defined ChIPQCexperiment object.) May be left unspecified, in which case no genomic feature analysis is performed. The following annotation specifiers are supported:

  "hg20"	Human, version 20
  "hg19"	Human, version 19
  "hg18"	Human, version 18
  "mm10"	Mouse, version 10
  "mm9"	Mouse, version 19
  "rn4"	Rat, version 4
  "ce6"	C. Elgans, version 6
  "dm3"	D. Melanogaster, version 3

  Alternatively, you can construct your own annotation; see the package Vignette for more information.

• chromosomes Specification of which chromosomes to use for computing QC statistics. If missing, the first chromosome which has a peak is checked. If NULL, all chromosomes will be checked (which may be time-consuming). This can be a character string (e.g. “chr18”) or a vector or list of character strings. If it is an integer or vector of integers, the chromosomes will be checked based on the order that they are listed in a peak set.

• mapQCth An integer representing a mapping quality score threshold. Only reads with mapping quality scores above this threshold will be used for some statistics.

• blacklist A GRanges object or filename specifying a bed file containing genomic regions that should be excluded from the analysis. If missing and the annotation is “hg19”, a default blacklist, blacklist_hg19 derived from the UCSC list, will be used. No blacklist is used if this is set to NULL, or is left missing and the annotation is not “hg19”.

• profileWin An integer indicating the width, in base pairs, of the window to be used for peak profiles. Peaks will be centered on their summits, and include half the window size upstream and half downstream of this point.

• fragmentLength An integer indicating the expected fragment length of the libraries. Optional, as this value will be computed.

• shifts A vector of values to try when computing optimal shift sizes.

• runCrossCor Compute cross-correlation in addition to cross-coverage. This will take more compute time, and is currently not used in the final report.

• verboseT TRUE or FALSE, specifying whether to report progress. Default is TRUE. When set to FALSE ChIPQC does not report any progress until complete.

Slots

AveragePeakSignal:

Object of class "list"

CrossCoverage:

Object of class "numeric"

CrossCorrelation:

Object of class "numeric"

SSD:

Object of class "numeric"

SSDBL:

Object of class "numeric"

CountsInPeaks:

Object of class "numeric"

CountsInBlackList:

Object of class "numeric"

CountsInFeatures:

Object of class "list"

PropInFeatures:

Object of class "list"

CoverageHistogram:

Object of class "numeric"

FlagAndTagCounts:

Object of class "numeric"

readlength:

Object of class "numeric"

seqnames:

Object of class "Rle"

ranges:

Object of class "IRanges"

strand:

Object of class "Rle"

elementMetadata:

Object of class "DataFrame"

seqinfo:

Object of class "Seqinfo"

metadata:

Object of class "list"

Extends

Class "GRanges"

Methods

averagepeaksignal

signature(object = "ChIPQCsample"): see averagepeaksignal.

coveragehistogram

signature(object = "ChIPQCsample"): see coveragehistogram.

crosscoverage

signature(object = "ChIPQCsample"): see crosscoverage.

flagtagcounts

signature(object = "ChIPQCsample"): see flagtagcounts.

fragmentlength

signature(object = "ChIPQCsample"): see fragmentlength.

FragmentLengthCrossCoverage

signature(object = "ChIPQCsample"): see FragmentLengthCrossCoverage.

frip

signature(object = "ChIPQCsample"): see frip.

mapped

signature(object = "ChIPQCsample"): see mapped.

reads

signature(object = "ChIPQCsample"): see reads.

duplicates

signature(object = "ChIPQCsample"): see duplicates.

duplicateRate

signature(object = "ChIPQCsample"): see duplicateRate.

Normalisedaveragepeaksignal

signature(object = "ChIPQCsample"): see Normalisedaveragepeaksignal.

peaks

signature(object = "ChIPQCsample"):see peaks.

readlength

signature(object = "ChIPQCsample"): see readlength.

ReadLengthCrossCoverage

signature(object = "ChIPQCsample"): see ReadLengthCrossCoverage.

RelativeCrossCoverage

signature(object = "ChIPQCsample"):see RelativeCrossCoverage.

ribl

signature(object = "ChIPQCsample"): see ribl.

rip

signature(object = "ChIPQCsample"): see rip.

show

signature(object = "ChIPQCsample"): see show.

ssd

signature(object = "ChIPQCsample"): see ssd.

regi

signature(object = "ChIPQCsample"): see regi.

plotCC

signature(object = "ChIPQCsample"): see plotCC.

plotCoverageHist

signature(object = "ChIPQCsample"): see plotCoverageHist.

plotFribl

signature(object = "ChIPQCsample"): see plotFribl.

plotPeakProfile

signature(object = "ChIPQCsample"): see plotPeakProfile.

plotRap

signature(object = "ChIPQCsample"): see plotRap.

plotRegi

signature(object = "ChIPQCsample"): see plotRegi.

Author(s)

Thomas Carroll and Rory Stark

References

Carroll TS, Liang Z, Salama R, Stark R and Santiago Id (in press). Impact of artefact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data. Frontiers in Genetics.

See Also

ChIPQC-package, ChIPQCsample

Examples

bamFile <- system.file("extdata", "ex1.bam", 
                        package="Rsamtools")
ex1 <- ChIPQCsample(bamFile,annotation=NULL)
readlength(ex1)
fragmentlength(ex1)

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