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

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Documentation for package ‘Basic4Cseq’ version 1.45.1

• 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