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

## Documentation for package ‘r3Cseq’ version 1.16.0

- 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