This package is an implementation of data analysis for the long-range interactions from 3C-seq assay.
|Author||Supat Thongjuea, MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, UK <email@example.com>|
|Date of publication||None|
|Maintainer||Supat Thongjuea <firstname.lastname@example.org>|
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