MMDiff: Statistical Testing for ChIP-Seq data sets

This package detects statistically significant difference between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD). WARNING: This package is deprecated, please use MMDiff2 instead.

Author
Gabriele Schweikert
Date of publication
None
Maintainer
Gabriele Schweikert <G.Schweikert@ed.ac.uk>
License
Artistic-2.0
Version
1.12.0

View on Bioconductor

Man pages

Cfp1Dists
Example DBA object used to illustrate usage of the MMDiff...
Cfp1Profiles
Example DBA object used to illustrate usage of the MMDiff...
compHistDists
Compute distances between pairs of histograms
detPeakPvals
Compute p-values for each peak based on distances between...
findOutliers
Find peaks with extreme count values
getNormFactors
Determine Normalisation factors
getPeakProfiles
Add histograms (binned read enrichment profiles) to an...
MMDiff-package
Statistical Testing for ChIP-Seq data sets
plotHistDists
plot MMD distances
plotPeak
plot read enrichment profiles at a specific peak for all...

Files in this package

MMDiff/.BBSoptions
MMDiff/DESCRIPTION
MMDiff/NAMESPACE
MMDiff/R
MMDiff/R/compDist.R
MMDiff/R/compDistWrapper.R
MMDiff/R/compHistDists.R
MMDiff/R/compHists.R
MMDiff/R/compPeakMatrix.R
MMDiff/R/compPeakTotalCounts.R
MMDiff/R/compute.pvalues.R
MMDiff/R/detPeakPvals.R
MMDiff/R/determineGroupComps.R
MMDiff/R/findComps.R
MMDiff/R/findOutliers.R
MMDiff/R/getNormFactors.R
MMDiff/R/getPeakIds4shift.R
MMDiff/R/getPeakProfiles.R
MMDiff/R/getReads.R
MMDiff/R/getReadsWrapper.R
MMDiff/R/getShift.R
MMDiff/R/mmd.R
MMDiff/R/plotHistDists.R
MMDiff/R/plotPeak.R
MMDiff/R/shiftReads.R
MMDiff/R/sortReads.R
MMDiff/R/zzz.R
MMDiff/build
MMDiff/build/vignette.rds
MMDiff/data
MMDiff/data/Cfp1Dists.RData
MMDiff/data/Cfp1Profiles.RData
MMDiff/data/datalist
MMDiff/inst
MMDiff/inst/doc
MMDiff/inst/doc/MMDiff.R
MMDiff/inst/doc/MMDiff.Rnw
MMDiff/inst/doc/MMDiff.pdf
MMDiff/man
MMDiff/man/Cfp1Dists.Rd
MMDiff/man/Cfp1Profiles.Rd
MMDiff/man/MMDiff-package.Rd
MMDiff/man/compHistDists.Rd
MMDiff/man/detPeakPvals.Rd
MMDiff/man/findOutliers.Rd
MMDiff/man/getNormFactors.Rd
MMDiff/man/getPeakProfiles.Rd
MMDiff/man/plotHistDists.Rd
MMDiff/man/plotPeak.Rd
MMDiff/vignettes
MMDiff/vignettes/ExamplePeak419.pdf
MMDiff/vignettes/GMDDists.pdf
MMDiff/vignettes/MMDDists.pdf
MMDiff/vignettes/MMDiff.Rnw
MMDiff/vignettes/MMDiff_bib.bib
MMDiff/vignettes/PearsonDists.pdf
MMDiff/vignettes/forwardVSReverse_WT_2.pdf
MMDiff/vignettes/strandShifts_WT_2.pdf