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MMDiff (version 1.8.0)

Statistical Testing for ChIP-Seq data sets

Description

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).

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Version

Version

1.8.0

License

Artistic-2.0

Maintainer

Gabriele Schweikert

Last Published

February 15th, 2017

Functions in MMDiff (1.8.0)

getPeakProfiles

Add histograms (binned read enrichment profiles) to an existing DBA object
findOutliers

Find peaks with extreme count values
getNormFactors

Determine Normalisation factors
MMDiff-package

Statistical Testing for ChIP-Seq data sets
compHistDists

Compute distances between pairs of histograms
detPeakPvals

Compute p-values for each peak based on distances between histograms
Cfp1Profiles

Example DBA object used to illustrate usage of the MMDiff package
Cfp1Dists

Example DBA object used to illustrate usage of the MMDiff package
plotHistDists

plot MMD distances
plotPeak

plot read enrichment profiles at a specific peak for all specified samples.