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


[Up] [Top]

Documentation for package ‘r3Cseq’ version 1.22.0

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