# Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data

## Documentation for package ‘Basic4Cseq’ version 1.10.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

checkRestrictionEnzymeSequence | Remove invalid 4C-seq reads from a SAM file
checkRestrictionEnzymeSequence-method | Remove invalid 4C-seq reads from a SAM file
chooseNearCisFragments | Choose fragments in a provided region around the viewpoint
chooseNearCisFragments-method | Choose fragments in a provided region around the viewpoint
createVirtualFragmentLibrary | Create a virtual fragment library from a provided genome and two restriction enzymes
createVirtualFragmentLibrary-method | Create a virtual fragment library from a provided genome and two restriction enzymes
Data4Cseq | Creating a Data4Cseq object
Data4Cseq-class | Class '"Data4Cseq"'
Data4Cseq-method | Creating a Data4Cseq object
drawDigestionFragmentHistogram | Visualize digestion fragments with a histogram
drawDigestionFragmentHistogram-method | Visualize digestion fragments with a histogram
drawHeatmap | Draw a heatmap-like multi-scale contact profile
drawHeatmap-method | Draw a heatmap-like multi-scale contact profile
exportVisualizationFragmentData | Export near-cis fragment data of a 'Data4Cseq' object
exportVisualizationFragmentData-method | Export near-cis fragment data of a 'Data4Cseq' object
getReadDistribution | Calculate the read distribution for a 4C-seq experiment
getReadDistribution-method | Calculate the read distribution for a 4C-seq experiment
giveEnzymeSequence | Provide the corresponding enzyme sequence for an enzyme name
giveEnzymeSequence-method | Provide the corresponding enzyme sequence for an enzyme name
importVisualizationFragmentData | Import visualization data from a file
importVisualizationFragmentData-method | Import visualization data from a file
liverData | Example 4C-seq data set of fetal liver data
liverDataRaw | Example 4C-seq data set of fetal liver data
nearCisFragments | Class '"Data4Cseq"'
nearCisFragments-method | Class '"Data4Cseq"'
nearCisFragments<- | Class '"Data4Cseq"'
nearCisFragments<--method | Class '"Data4Cseq"'
normalizeFragmentData | Normalize near-cis fragment data read count
normalizeFragmentData-method | Normalize near-cis fragment data read count
plotTransInteractions | Visualize trans interaction intervals
plotTransInteractions-method | Visualize trans interaction intervals
pointsOfInterest | Class '"Data4Cseq"'
pointsOfInterest-method | Class '"Data4Cseq"'
pointsOfInterest<- | Class '"Data4Cseq"'
pointsOfInterest<--method | Class '"Data4Cseq"'
prepare4CseqData | Alignment and filtering of raw 4C-seq data
prepare4CseqData-method | Alignment and filtering of raw 4C-seq data
printBEDFragmentLibrary | Print a BED-file fragment library
printBEDFragmentLibrary-method | Print a BED-file fragment library
printWigFile | Print a wig file from 4C-seq read data
printWigFile-method | Print a wig file from 4C-seq read data
rawFragments | Class '"Data4Cseq"'
rawFragments-method | Class '"Data4Cseq"'
rawFragments<- | Class '"Data4Cseq"'
rawFragments<--method | Class '"Data4Cseq"'
rawReads | Class '"Data4Cseq"'
rawReads-method | Class '"Data4Cseq"'
rawReads<- | Class '"Data4Cseq"'
rawReads<--method | Class '"Data4Cseq"'
readLength | Class '"Data4Cseq"'
readLength-method | Class '"Data4Cseq"'
readLength<- | Class '"Data4Cseq"'
readLength<--method | Class '"Data4Cseq"'
readPointsOfInterestFile | Read a file with coordinates of marker points
readPointsOfInterestFile-method | Read a file with coordinates of marker points
readsToFragments | Determine fragment coverage of a 4C-seq fragment library
readsToFragments-method | Determine fragment coverage of a 4C-seq fragment library
simulateDigestion | Simulate the digestion of a genome
simulateDigestion-method | Simulate the digestion of a genome
viewpointChromosome | Class '"Data4Cseq"'
viewpointChromosome-method | Class '"Data4Cseq"'
viewpointChromosome<- | Class '"Data4Cseq"'
viewpointChromosome<--method | Class '"Data4Cseq"'
viewpointInterval | Class '"Data4Cseq"'
viewpointInterval-method | Class '"Data4Cseq"'
viewpointInterval<- | Class '"Data4Cseq"'
viewpointInterval<--method | Class '"Data4Cseq"'
visualizeViewpoint | Draw a near-cis coverage plot for 4C-seq data
visualizeViewpoint-method | Draw a near-cis coverage plot for 4C-seq data