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MMDiff (version 1.12.0)

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). WARNING: This package is deprecated, please use MMDiff2 instead.

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Version

Version

1.12.0

License

Artistic-2.0

Maintainer

Gabriele Schweikert

Last Published

February 15th, 2017

Functions in MMDiff (1.12.0)

plot MMD distances

Find peaks with extreme count values

Example DBA object used to illustrate usage of the MMDiff package

DBAmmd Object for Cfp1 example

Compute distances between pairs of histograms

DBAmmd-Accessors

Extract data from DBAmmd objects

Peaks for Cfp1-data set

Example DBA object used to illustrate usage of the MMDiff package

Statistical Testing for ChIP-Seq data sets

Compute Peak histograms

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

Determine Normalisation factors

getPeakProfiles

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

compute p-values

Compute distances between Peaks

estimateFragmentCenters

estimate center of fragments

ui component for interactive visualization of MMD,GMD and Pearson Difference as well as plotting peaks

Get reads from indexed bam files for defined regions

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

runShinyMMDiff2

Shiny Application for interactive visualization of MMD,GMD and Pearson Difference as well as plotting peaks

Generics for DBAmmd-Class

Shiny server code for interactive visualization of MMD distances, peak plots, and MMD distances by sample.