Man pages for supatt-lab/r3Cseq
Analysis of Chromosome Conformation Capture and Next-generation Sequencing (3C-seq)
| calculateBatchRPM | calculate read per million (RPM) for replicates analysis |
| calculateRPM | calculate read per million (RPM) |
| contrCoverage | This method has been removed. |
| contrInteractionRegions | get interaction regions from the control |
| contrRawData | Accessors for the 'contrRawData' slot of a r3Cseq object. |
| contrReadCount | get read count per region for the control |
| contrRPM | get read per million (RPM) for the control |
| enzymeDb | Rebase The Restriction Enzyme Database |
| expCoverage | This method has been removed. |
| expInteractionRegions | get interaction regions from the experiment |
| export3Cseq2bedGraph | export interaction regions to the 'bedGraph' format |
| export3CseqRawReads2bedGraph | export the interaction signal from the raw reads to the... |
| exportBatchInteractions2text | export identified interaction regions to the tab separated... |
| exportInteractions2text | export identified interaction regions to the tab separated... |
| expRawData | Accessors for the 'expRawData' slot of a r3Cseq object. |
| expReadCount | get read count per region for the experiment |
| expRPM | get read per million (RPM) for the experiment |
| generate3CseqReport | generate reports for analysis results from r3Cseq |
| getBatchInteractions | calculate z-score, assign p-value and q-value for each... |
| getBatchRawReads | Get aligned reads from the replicates BAM files |
| getBatchReadCountPerRestrictionFragment | count reads for replicates analysis |
| getBatchReadCountPerWindow | count reads per window size for replicates analysis |
| getContrInteractionsInRefseq | identified significant interaction regions for RefSeq genes |
| getCoverage | This method has been removed. |
| getExpInteractionsInRefseq | identified significant interaction regions for RefSeq genes |
| getInteractions | calculate z-score, assign p-value and q-value for each... |
| getRawReads | Get aligned reads from the BAM file |
| getReadCountPerRestrictionFragment | count reads per resitrcition fragment |
| getReadCountPerWindow | count reads per window size |
| getViewpoint | 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. |
| plotDomainogramNearViewpoint | Plot domainogram of interaction regions near the viewpoint |
| plotInteractionsNearViewpoint | Plot identified interaction regions near the viewpoint |
| plotInteractionsPerChromosome | Plot interaction regions per each chromosome of interest |
| plotOverviewInteractions | Plot overview of identified interaction regions for... |
| r3Cseq-class | r3Cseq objects |
| r3CseqCommon-class | r3CseqCommon objects |
| r3CseqInBatch-class | r3CseqInBatch objects |
| rn5refGene | rn5's refGenes |
