Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)

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Documentation for package ‘r3Cseq’ version 1.51.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

calculateBatchRPM	calculate read per million (RPM) for replicates analysis
calculateBatchRPM-method	calculate read per million (RPM) for replicates analysis
calculateRPM	calculate read per million (RPM)
calculateRPM-method	calculate read per million (RPM)
contrCoverage	This method has been removed.
contrCoverage-method	This method has been removed.
contrInteractionRegions	get interaction regions from the control
contrInteractionRegions-method	get interaction regions from the control
contrRawData	Accessors for the 'contrRawData' slot of a r3Cseq object.
contrRawData-method	Accessors for the 'contrRawData' slot of a r3Cseq object.
contrRawData<-	Accessors for the 'contrRawData' slot of a r3Cseq object.
contrRawData<--method	Accessors for the 'contrRawData' slot of a r3Cseq object.
contrReadCount	get read count per region for the control
contrReadCount-method	get read count per region for the control
contrRPM	get read per million (RPM) for the control
contrRPM-method	get read per million (RPM) for the control
enzymeDb	Rebase The Restriction Enzyme Database
expCoverage	This method has been removed.
expCoverage-method	This method has been removed.
expInteractionRegions	get interaction regions from the experiment
expInteractionRegions-method	get interaction regions from the experiment
export3Cseq2bedGraph	export interaction regions to the 'bedGraph' format
export3Cseq2bedGraph-method	export interaction regions to the 'bedGraph' format
export3CseqRawReads2bedGraph	export the interaction signal from the raw reads to the 'bedGraph' format
export3CseqRawReads2bedGraph-method	export the interaction signal from the raw reads to the 'bedGraph' format
exportBatchInteractions2text	export identified interaction regions to the tab separated format for replicates analysis
exportBatchInteractions2text-method	export identified interaction regions to the tab separated format for replicates analysis
exportInteractions2text	export identified interaction regions to the tab separated format
exportInteractions2text-method	export identified interaction regions to the tab separated format
expRawData	Accessors for the 'expRawData' slot of a r3Cseq object.
expRawData-method	Accessors for the 'expRawData' slot of a r3Cseq object.
expRawData<-	Accessors for the 'expRawData' slot of a r3Cseq object.
expRawData<--method	Accessors for the 'expRawData' slot of a r3Cseq object.
expReadCount	get read count per region for the experiment
expReadCount-method	get read count per region for the experiment
expRPM	get read per million (RPM) for the experiment
expRPM-method	get read per million (RPM) for the experiment
generate3CseqReport	generate reports for analysis results from r3Cseq
generate3CseqReport-method	generate reports for analysis results from r3Cseq
getBatchInteractions	calculate z-score, assign p-value and q-value for each interaction region for replicates data sets
getBatchInteractions-method	calculate z-score, assign p-value and q-value for each interaction region for replicates data sets
getBatchRawReads	Get aligned reads from the replicates BAM files
getBatchRawReads-method	Get aligned reads from the replicates BAM files
getBatchReadCountPerRestrictionFragment	count reads for replicates analysis
getBatchReadCountPerRestrictionFragment-method	count reads for replicates analysis
getBatchReadCountPerWindow	count reads per window size for replicates analysis
getBatchReadCountPerWindow-method	count reads per window size for replicates analysis
getContrInteractionsInRefseq	identified significant interaction regions for RefSeq genes
getContrInteractionsInRefseq-method	identified significant interaction regions for RefSeq genes
getCoverage	This method has been removed.
getCoverage-method	This method has been removed.
getExpInteractionsInRefseq	identified significant interaction regions for RefSeq genes
getExpInteractionsInRefseq-method	identified significant interaction regions for RefSeq genes
getInteractions	calculate z-score, assign p-value and q-value for each interaction region
getInteractions-method	calculate z-score, assign p-value and q-value for each interaction region
getRawReads	Get aligned reads from the BAM file
getRawReads-method	Get aligned reads from the BAM file
getReadCountPerRestrictionFragment	count reads per resitrcition fragment
getReadCountPerRestrictionFragment-method	count reads per resitrcition fragment
getReadCountPerWindow	count reads per window size
getReadCountPerWindow-method	count reads per window size
getViewpoint	get the viewpoint of 3C-seq data
getViewpoint-method	get the viewpoint of 3C-seq data
hg18refGene	hg18's refGenes
hg19refGene	hg19's refGenes
mm10refGene	mm10's refGenes
mm9refGene	mm9's refGenes
Myb_prom_FB	Myb_prom_FB a data set for the example of r3Cseq analysis
Myb_prom_FL	Myb_prom_FL a data set for the example of r3Cseq analysis
plot3Cecdf	This method has been removed.
plot3Cecdf-method	This method has been removed.
plotDomainogramNearViewpoint	Plot domainogram of interaction regions near the viewpoint
plotDomainogramNearViewpoint-method	Plot domainogram of interaction regions near the viewpoint
plotInteractionsNearViewpoint	Plot identified interaction regions near the viewpoint
plotInteractionsNearViewpoint-method	Plot identified interaction regions near the viewpoint
plotInteractionsPerChromosome	Plot interaction regions per each chromosome of interest
plotInteractionsPerChromosome-method	Plot interaction regions per each chromosome of interest
plotOverviewInteractions	Plot overview of identified interaction regions for genome-wide
plotOverviewInteractions-method	Plot overview of identified interaction regions for genome-wide
r3Cseq	r3Cseq objects
r3Cseq-class	r3Cseq objects
r3CseqCommon	r3CseqCommon objects
r3CseqCommon-class	r3CseqCommon objects
r3CseqInBatch	r3CseqInBatch objects
r3CseqInBatch-class	r3CseqInBatch objects
rn5refGene	rn5's refGenes