methylSig v0.99.4

User Changes

• Add direction column to diff_dss_test() output
  • Harmonizes with other diff functions.
  • In the case of a numerical covariate, direction is assigned "Hyper" or "Hypo"
• diff_dss_test() used case_meth and control_meth instead of meth_case and meth_control like the other diff functions.

methylSig v0.99.1

Backend

• Various code style alterations for Bioconductor.

Bugfixes

• Pass a logical vector to cols parameter of DelayedMatrixStats::rowSums2() instead of column names.

methylSig v0.99.0

Changes in anticipation of submission to Bioconductor.

• Refactor functions and workflow from pre-0.99.0 releases
  • methylSigReadData() replaced with the functions:
    • bsseq::read.bismark()
    • filter_loci_by_coverage()
    • filter_loci_by_location()
  • methylSigTile() replaced with the functions:
    • tile_by_regions()
    • tile_by_windows()
  • Differential testing should be preceded by the following for group tests:
    • filter_loci_by_group_coverage()
  • binomialDiffCalc() is replaced by diff_binomial()
  • methylSigCalc() is replaced by diff_methylSig()
  • methylSigDSS() is replaced by diff_dss_fit() and diff_dss_test()
• See "Using methylSig" vignette for full example.
• See "Updating methylSig Code" vignette for how to retrofit pre-0.99.0 code.

methylSig v0.5.2

• Reintroduce Seqinfo via the assembly parameter of methylSigReadData
  • If NA, allow user to continue, but warn that tiling and annotation cannot work unless the user manually assigns Seqinfo to the BSseq object.
  • If assembly is unsupported in GenomeInfoDb::fetchExtendedChromInfoFromUCSC, act as if it was set to NA.
  • If assembly is supported, use it.
  • seqinfo persists through tiling, tests for different methylation, and annotation.

methylSig v0.5.1

• Minor bugfix in methylSigTile() function. Cannot reproduce everywhere, but sometimes when a chromosome has no entries in the meth object, the tiling function failed. Now check for entries on the chromosome.

methylSig v0.5.0

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.

methylSig v0.4.4 (minor bugfix)

• Fixed a typo in a method for methylSigData objects.

methylSig v0.4.3 (major bugfix)

Bug in methylSigReadData()

• The problem: In #14, @bmreilly observed that adding more samples resulted in fewer sites tested for DM.
• The reason: 060381b moved the minCount/maxCount filter from methylSigReadDataSingleFile() to methylSigReadData() after destranding. This way destranding would rescue +/- sites that individually were < minCount, but when destranded were > minCount. This fix introduced another bug whereby a site in any sample failing minCount/maxCount would remove this site from every sample. This behavior is consistent with the behavior in #14.
• The fix: This release refactors methylSigReadData() and methylSigReadDataSingleFile() so that destranding and the minCount/maxCount filter are in methylSigReadDataSingleFile(), and only the site in the offending sample will be minCount/maxCount filtered. Included in the fix are new unit tests and new test files to fully ensure the behavior we expect.

Accessor for findOverlaps()

• 9ba232c accesses queryHits with accessor function queryHits() instead of slots @ when filtering SNPs. Accessing with @ was causing Travis-CI build failures.

methylSig v0.4.2 (minor bugfixes)

This release fixes a minor bug in methylSigReadData() where the function would fail if a sample had no sites < minCount or > maxCount. This is unlikely to happen in actual data, but is nevertheless a bug.

methylSig v0.4.1 (major bugfixes)

This release fixes the following bugs which impact methylSig results:

• Two sites with coverage < minCount, but combined coverage > minCount after destranding were not rescued. For example, if minCount = 10 and both sites had coverage 5, the destranded site would not make it through the filter.
• Tiling with methylSigTile() erroneously reported NAs for samples where regions contained CpGs that the sample did not cover. For example, if a region contained 3 CpGs, and one sample had NA (i.e. no coverage) at just one of the CpGs, the aggregation of the data over the CpGs in the region would give NA for that sample. This had the effect of throwing away a lot of data.
• Tiling with methylSigTile() extended windows past the end of a chromosome in certain cases. Since methylSig is genome agnostic, this problem is solved by making the last window smaller (2bp) so as not to cross a chromosome boundary. This can create problems if you try making a bigBED file out of the results.