SimBindProfiles: Similar Binding Profiles

SimBindProfiles identifies common and unique binding regions in genome tiling array data. This package does not rely on peak calling, but directly compares binding profiles processed on the same array platform. It implements a simple threshold approach, thus allowing retrieval of commonly and differentially bound regions between datasets as well as events of compensation and increased binding.

Author
Bettina Fischer, Enrico Ferrero, Robert Stojnic, Steve Russell
Date of publication
None
Maintainer
Bettina Fischer <bef22@cam.ac.uk>
License
GPL-3
Version
1.12.0

View on Bioconductor

Man pages

compensationRegions
Classify two Binding Profiles - Compensation
eSetScatterPlot
Scatterplot of ExpressionSet object
findBoundCutoff
Find the bound.cutoff
increasedBindingRegions
Classify two Binding Profiles - Increased Binding
pairwiseRegions
Classify two Binding Profiles
plotBoundProbes
Plot coloured bound probes
probeAnnoFromESet
Build a probeAnno from ExpressionSet
probeLengthPlot
Plot the probe length frequency
readSgrFiles
Read sgr data
SGR
A Sample Data object
SimBindProfiles-package
Similar Binding Profiles, identifies common and unique...
threewayRegions
Classify three Binding Profiles

Files in this package

SimBindProfiles/DESCRIPTION
SimBindProfiles/NAMESPACE
SimBindProfiles/R
SimBindProfiles/R/compensationRegions.R
SimBindProfiles/R/eSetScatterPlot.R
SimBindProfiles/R/filterRegionsPairwise.R
SimBindProfiles/R/filterRegionsThreeway.R
SimBindProfiles/R/findBoundCutoff.R
SimBindProfiles/R/increasedBindingRegions.R
SimBindProfiles/R/normalNull.R
SimBindProfiles/R/pairwiseRegions.R
SimBindProfiles/R/plotBoundProbes.R
SimBindProfiles/R/probeAnnoFromESet.R
SimBindProfiles/R/probeLengthPlot.R
SimBindProfiles/R/readSgrFiles.R
SimBindProfiles/R/setBoundFlag.R
SimBindProfiles/R/setFlagCompensation.R
SimBindProfiles/R/setFlagIncreasedBinding.R
SimBindProfiles/R/setPairwiseClassFlag.R
SimBindProfiles/R/setThreewayClassFlag.R
SimBindProfiles/R/threewayRegions.R
SimBindProfiles/R/twoGaussiansNull.BF.R
SimBindProfiles/build
SimBindProfiles/build/vignette.rds
SimBindProfiles/data
SimBindProfiles/data/SGR.RData
SimBindProfiles/data/datalist
SimBindProfiles/data/precomputed.RData
SimBindProfiles/inst
SimBindProfiles/inst/doc
SimBindProfiles/inst/doc/SimBindProfiles.R
SimBindProfiles/inst/doc/SimBindProfiles.Rnw
SimBindProfiles/inst/doc/SimBindProfiles.pdf
SimBindProfiles/inst/extdata
SimBindProfiles/inst/extdata/DDam_trunc.txt
SimBindProfiles/inst/extdata/SoxN-DDam_trunc.txt
SimBindProfiles/inst/extdata/SoxNDam_trunc.txt
SimBindProfiles/man
SimBindProfiles/man/SGR.Rd
SimBindProfiles/man/SimBindProfiles-package.Rd
SimBindProfiles/man/compensationRegions.Rd
SimBindProfiles/man/eSetScatterPlot.Rd
SimBindProfiles/man/findBoundCutoff.Rd
SimBindProfiles/man/increasedBindingRegions.Rd
SimBindProfiles/man/pairwiseRegions.Rd
SimBindProfiles/man/plotBoundProbes.Rd
SimBindProfiles/man/probeAnnoFromESet.Rd
SimBindProfiles/man/probeLengthPlot.Rd
SimBindProfiles/man/readSgrFiles.Rd
SimBindProfiles/man/threewayRegions.Rd
SimBindProfiles/vignettes
SimBindProfiles/vignettes/Makefile
SimBindProfiles/vignettes/SimBindProfiles-Bibliography.bib
SimBindProfiles/vignettes/SimBindProfiles.Rnw
SimBindProfiles/vignettes/SimBindProfiles.tex