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 |