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

## Documentation for package ‘r3Cseq’ version 1.4.0

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.

## 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