Basic4Cseq: Basic4Cseq: an R/Bioconductor package for analyzing 4C-seq data
Version 1.12.0

Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

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AuthorCarolin Walter
Bioconductor views QualityControl Visualization
Date of publicationNone
MaintainerCarolin Walter <carolin.walter@uni-muenster.de>
LicenseLGPL-3
Version1.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("Basic4Cseq")

Man pages

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

Functions

Data4Cseq Man page
Data4Cseq,character,numeric,numeric,data.frame,GAlignments-metho Man page
Data4Cseq,character,numeric,numeric,missing,missing-method Man page
Data4Cseq-class Man page
basic4CPlot Source code
checkRestrictionEnzymeSequence Man page Source code
checkRestrictionEnzymeSequence,character,character-method Man page
chooseNearCisFragments Man page Source code
chooseNearCisFragments,Data4Cseq,numeric-method Man page
createVirtualFragmentLibrary Man page
createVirtualFragmentLibrary,BSgenome,character,character,numeri Man page
createVirtualFragmentLibrary,DNAString,character,character,numer Man page
createVirtualFragmentLibraryMain Source code
createVirtualFragmentLibrary_BSgenome Source code
createVirtualFragmentLibrary_DNAString Source code
drawDigestionFragmentHistogram Man page Source code
drawDigestionFragmentHistogram,data.frame-method Man page
drawHeatmap Man page
drawHeatmap,Data4Cseq-method Man page
drawHeatmap,data.frame-method Man page
drawHeatmapMain Source code
drawHeatmap_Data4Cseq Source code
drawHeatmap_DataFrame Source code
drawMetaData Source code
exportVisualizationFragmentData Man page Source code
exportVisualizationFragmentData,Data4Cseq,character-method Man page
formatFragmentDataMain Source code
formatFragmentData_Data4Cseq Source code
formatFragmentData_DataFrame Source code
getReadDistribution Man page Source code
getReadDistribution,Data4Cseq-method Man page
giveEnzymeSequence Man page Source code
giveEnzymeSequence,character,character-method Man page
giveWigDataChromosome Source code
importVisualizationFragmentData Man page
importVisualizationFragmentData,character-method Man page
liverData Man page
liverDataRaw Man page
mportVisualizationFragmentData Source code
nearCisFragments Man page
nearCisFragments,Data4Cseq-method Man page
nearCisFragments<- Man page
nearCisFragments<-,Data4Cseq,data.frame-method Man page
normalizeFragmentData Man page Source code
normalizeFragmentData,Data4Cseq-method Man page
plotTransInteractions Man page
plotTransInteractions,character,character,numeric,character-meth Man page
plotTransInteractions,data.frame,character,numeric,data.frame-me Man page
plotTransInteractionsMain Source code
plotTransInteractions_Character Source code
plotTransInteractions_DataFrame Source code
pointsOfInterest Man page
pointsOfInterest,Data4Cseq-method Man page
pointsOfInterest<- Man page
pointsOfInterest<-,Data4Cseq,data.frame-method Man page
prepare4CseqData Man page Source code
prepare4CseqData,character,character,character,character-method Man page
printBEDFragmentLibrary Man page Source code
printBEDFragmentLibrary,character,character-method Man page
printWigFile Man page Source code
printWigFile,Data4Cseq-method Man page
rawFragments Man page
rawFragments,Data4Cseq-method Man page
rawFragments<- Man page
rawFragments<-,Data4Cseq,data.frame-method Man page
rawReads Man page
rawReads,Data4Cseq-method Man page
rawReads<- Man page
rawReads<-,Data4Cseq,GAlignments-method Man page
readLength Man page
readLength,Data4Cseq-method Man page
readLength<- Man page
readLength<-,Data4Cseq,numeric-method Man page
readPointsOfInterestFile Man page Source code
readPointsOfInterestFile,character-method Man page
readsToFragments Man page Source code
readsToFragments,Data4Cseq,character-method Man page
simulateDigestion Man page
simulateDigestion,character,character,BSgenome-method Man page
simulateDigestion,character,character,character-method Man page
simulateDigestionChromosome_DNAString Source code
simulateDigestionChromosome_MaskedDNAString Source code
simulateDigestion_BSgenome Source code
simulateDigestion_Character Source code
splitChromosome_DNAString Source code
viewpointChromosome Man page
viewpointChromosome,Data4Cseq-method Man page
viewpointChromosome<- Man page
viewpointChromosome<-,Data4Cseq,character-method Man page
viewpointInterval Man page
viewpointInterval,Data4Cseq-method Man page
viewpointInterval<- Man page
viewpointInterval<-,Data4Cseq,numeric-method Man page
visualizeViewpoint Man page
visualizeViewpoint,Data4Cseq-method Man page
visualizeViewpoint,data.frame-method Man page
visualizeViewpointMain Source code
visualizeViewpoint_Data4Cseq Source code
visualizeViewpoint_DataFrame Source code

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.r
R/AllGenerics.r
R/checkRestrictionEnzymeSequence.r
R/chooseNearCisFragments.r
R/createVirtualFragmentLibrary.r
R/drawHeatmap.r
R/formatFragmentData.r
R/getReadDistribution.r
R/giveEnzymeSequence.r
R/methods-Data4Cseq.r
R/normalizeFragmentData.r
R/plotTransInteractions.r
R/prepare4CseqData.r
R/printBEDFragmentLibrary.r
R/printWigFile.r
R/readPointsOfInterestFile.r
R/readsToFragments.r
R/simulateDigestion.r
R/visualizeViewpoint.r
build
build/vignette.rds
data
data/liverData.RData
data/liverDataRaw.RData
inst
inst/doc
inst/doc/vignette.R
inst/doc/vignette.Rnw
inst/doc/vignette.pdf
inst/extdata
inst/extdata/RCircos_GRCm38_ideogram.csv
inst/extdata/RCircos_HG19_ideogram.csv
inst/extdata/enzymeData.csv
inst/extdata/fetalLiverCutter.sam
inst/extdata/fetalLiverShort.bam
inst/extdata/fetalLiverVP.bed
inst/extdata/fetalLiver_finalFragments.csv
inst/extdata/transInteractionData.txt
inst/extdata/veryShortExample.fastq
inst/extdata/veryShortLib.csv
inst/extdata/veryShortReference.fasta
inst/extdata/veryShortReference.fasta.amb
inst/extdata/veryShortReference.fasta.ann
inst/extdata/veryShortReference.fasta.bwt
inst/extdata/veryShortReference.fasta.pac
inst/extdata/veryShortReference.fasta.sa
inst/extdata/vfl_aagctt_catg_mm9_54_vp.csv
man
man/Data4Cseq-class.Rd
man/Data4Cseq.Rd
man/checkRestrictionEnzymeSequence.Rd
man/chooseNearCisFragments.Rd
man/createVirtualFragmentLibrary.Rd
man/drawDigestionFragmentHistogram.Rd
man/drawHeatmap.Rd
man/exportVisualizationFragmentData.Rd
man/getReadDistribution.Rd
man/giveEnzymeSequence.Rd
man/importVisualizationFragmentData.Rd
man/liverData.Rd
man/liverDataRaw.Rd
man/normalizeFragmentData.Rd
man/plotTransInteractions.Rd
man/prepare4CseqData.Rd
man/printBEDFragmentLibrary.Rd
man/printWigFile.Rd
man/readPointsOfInterestFile.Rd
man/readsToFragments.Rd
man/simulateDigestion.Rd
man/visualizeViewpoint.Rd
vignettes
vignettes/images
vignettes/images/drawHeatmap_Output.pdf
vignettes/images/visualizeViewpoint_Output.pdf
vignettes/vignette.Rnw
Basic4Cseq documentation built on May 20, 2017, 10:19 p.m.