MMDiff: Statistical Testing for ChIP-Seq data sets
Version 1.12.0

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.

Browse man pages Browse package API and functions Browse package files

AuthorGabriele Schweikert
Date of publicationNone
MaintainerGabriele Schweikert <G.Schweikert@ed.ac.uk>
LicenseArtistic-2.0
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("MMDiff")

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...

Functions

Cfp1Dists Man page
Cfp1Profiles Man page
MMDiff Man page
MMDiff-package Man page
compHistDists Man page
detPeakPvals Man page
findOutliers Man page
getNormFactors Man page
getPeakProfiles Man page
plotHistDists Man page
plotPeak Man page

Files

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
MMDiff documentation built on Oct. 5, 2016, 4:28 a.m.