Man pages for r3Cseq
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)

calculateBatchRPMcalculate read per million (RPM) for replicates analysis
calculateRPMcalculate read per million (RPM)
contrCoverageThis method has been removed.
contrInteractionRegionsget interaction regions from the control
contrRawDataAccessors for the 'contrRawData' slot of a r3Cseq object.
contrReadCountget read count per region for the control
contrRPMget read per million (RPM) for the control
enzymeDbRebase The Restriction Enzyme Database
expCoverageThis method has been removed.
expInteractionRegionsget interaction regions from the experiment
export3Cseq2bedGraphexport interaction regions to the 'bedGraph' format
export3CseqRawReads2bedGraphexport the interaction signal from the raw reads to the...
exportBatchInteractions2textexport identified interaction regions to the tab separated...
exportInteractions2textexport identified interaction regions to the tab separated...
expRawDataAccessors for the 'expRawData' slot of a r3Cseq object.
expReadCountget read count per region for the experiment
expRPMget read per million (RPM) for the experiment
generate3CseqReportgenerate reports for analysis results from r3Cseq
getBatchInteractionscalculate z-score, assign p-value and q-value for each...
getBatchRawReadsGet aligned reads from the replicates BAM files
getBatchReadCountPerRestrictionFragmentcount reads for replicates analysis
getBatchReadCountPerWindowcount reads per window size for replicates analysis
getContrInteractionsInRefseqidentified significant interaction regions for RefSeq genes
getCoverageThis method has been removed.
getExpInteractionsInRefseqidentified significant interaction regions for RefSeq genes
getInteractionscalculate z-score, assign p-value and q-value for each...
getRawReadsGet aligned reads from the BAM file
getReadCountPerRestrictionFragmentcount reads per resitrcition fragment
getReadCountPerWindowcount reads per window size
getViewpointget the viewpoint of 3C-seq data
hg18refGenehg18's refGenes
hg19refGenehg19's refGenes
mm10refGenemm10's refGenes
mm9refGenemm9's refGenes
Myb_prom_FBMyb_prom_FB a data set for the example of r3Cseq analysis
Myb_prom_FLMyb_prom_FL a data set for the example of r3Cseq analysis
plot3CecdfThis method has been removed.
plotDomainogramNearViewpointPlot domainogram of interaction regions near the viewpoint
plotInteractionsNearViewpointPlot identified interaction regions near the viewpoint
plotInteractionsPerChromosomePlot interaction regions per each chromosome of interest
plotOverviewInteractionsPlot overview of identified interaction regions for...
r3Cseq-classr3Cseq objects
r3CseqCommon-classr3CseqCommon objects
r3CseqInBatch-classr3CseqInBatch objects
rn5refGenern5's refGenes
r3Cseq documentation built on Nov. 17, 2017, 10:12 a.m.