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methylSig v0.5.0
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@rcavalcante rcavalcante released this 06 Dec 15:06
v0.5.0
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NOTE: This version of methylSig only works for R 3.4.z with Bioconductor 3.6. It may work for earlier paired versions, but I make no guarantees. A feature change in the bsseq Bioconductor package in Bioc >= 3.7 does not allow BSseq-class objects whose GRanges are not points, and this breaks the tiling functionality of methylSig. For Bioc 3.9 we hope to have this issue fixed.

New Features

  • Annotations are now done with the annotatr Bioconductor package.

User-level Changes

  • methylSig v0.5.0 reuses Bioconductor classes rather than the home-spun classes of earlier versions. This will improve maintainability greatly.

  • The methylSigReadData() function now is a wrapper for the bsseq::read.bismark() function, obviating the need to transform the input data in anyway. The output is a BSseq-class object.

  • As before, filtering for common SNPs (hg19 only), minCount, and maxCount are available. Destranding also remains.

  • The result of any of the tests for differential methylation are now GRanges-class objects.

  • Built-in example data is now known as sample_data.

Bug Fixes

  • Fixed a mistake in methylSig.tfbsEnrichTest() that mistakenly referred referred to tfbsInfo parameter as tfbs.

Removed Features

  • Removed plotting functions for retooling.
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