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

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Documentation for package ‘r3Cseq’ version 1.4.0

Help Pages

calculateRPM calculate read per million (RPM)
calculateRPM-method calculate read per million (RPM)
contrCoverage Get the coverage for 3C-seq data from the control
contrCoverage-method Get the coverage for 3C-seq data from the control
contrInteractionRegions get interaction regions from the control
contrInteractionRegions-method get interaction regions from the control
contrRPM get read per million (RPM) for the control
contrRPM-method get read per million (RPM) for the control
enzyme.db Rebase The Restriction Enzyme Database
expCoverage Get the coverage for 3C-seq data from the experiment
expCoverage-method Get the coverage for 3C-seq data from the experiment
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
exportInteractions2text export interaction regions to the tab separated format
exportInteractions2text-method export interaction regions to the tab separated format
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
getCoverage Coverage for 3C-seq data
getCoverage-method Coverage for 3C-seq data
getInteractions assign p-value and fold change to candidate interaction regions
getInteractions-method assign p-value and fold change to candidate interaction regions
getReadCountPerRestrictionFragment get read count per restriction fragment for 3C-seq data
getReadCountPerRestrictionFragment-method get read count per restriction fragment for 3C-seq data
getViewpoint get the viewpoint of 3C-seq data
getViewpoint-method get the viewpoint of 3C-seq data
my.data a simple example of r3Cseq object
plot3Cecdf Plot the empirical distribution of interaction regions
plot3Cecdf-method Plot the empirical distribution of interaction regions
plotInteractionsNearViewpoint Plot candidate interaction regions near the viewpoint
plotInteractionsNearViewpoint-method Plot candidate 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 the overview of interaction regions for the genome-wide
plotOverviewInteractions-method Plot the overview of interaction regions for the genome-wide
r3Cseq r3Cseq objects
r3Cseq-class r3Cseq objects