Changes in version 1.8: o preprocessQuantile(object) would fail if object was a GenomicMethylSet. This is now fixed. o Cleanup of Rd markdown in various help files. o estimateCellCounts would throw an error. This is now fixed. The function arguments have changed. o Bug in cpgCollapse led to incorrect results. Your output is affected if table(granges(output[[1]])$type) is all 'OpenSea'. Reported by Florence Cavalli . o Encapsulated the example for estimateCellCounts() in 'dontrun', to disable it on the build servers. o preprocessQuantile would work as if removeBadSamples=TRUE no matter the value of the argument. o Fixing replace bug in fixMethOutliers; it would not work on the output of preprocessSWAN. Reported by David McGaughey o The function mapToGenome would return something that looked like an unordered GenomicMethylSet. Actually, loci were correctly ordered within chromosomes, the issue had to do with whether the chromosomes were ordered as chr1, chr2, chr3 (used in minfi) or chr1, chr10, chr11 (lexigraphically). Reported by Florence Cavalli . o Switched to using new author format in DESCRIPTION. Changes in version 1.7: o Added getMethSignal(), a convenience function for programming. o Changed the argument name of "type" to "what" for getMethSignal(). o Added the class "RatioSet", like "GenomicRatioSet" but without the genome information. o Bugfixes to the "GenomicRatioSet()" constructor. o Added the method ratioConvert(), for converting a "MethylSet" to a "RatioSet" or a "GenomicMethylSet" to a "GenomicRatioSet". o Fixed an issue with GenomicMethylSet() and GenomicRatioSet() caused by a recent change to a non-exported function in the GenomicRanges package (Reported by Gustavo Fernandez Bayon ). o Added fixMethOutliers for thresholding extreme observations in the [un]methylation channels. o Added getSex, addSex, plotSex for estimating sex of the samples. o Added getQC, addQC, plotQC for a very simple quality control measure. o Added minfiQC for a one-stop function for quality control measures. o Changed some verbose=TRUE output in various functions. o Added preprocessQuantile. o Added bumphunter method for "GenomicRatioSet". o Handling signed zero in minfi:::.digestMatrix which caused unit tests to fail on Windows. o addSex and addQC lead to sampleNames() being dropped because of a likely bug in cbind(DataFrame, DataFrame). Work-around has been implemented. o Re-ran the test data generator. o Fixed some Depends and Imports issues revealed by new features of R CMD check. o Added blockFinder and cpgCollapse. o (internal) added convenience functions for argument checking. o Exposed and re-wrote getAnnotation(). o Changed getLocations() from being a method to a simple function. Arguments have been removed (for example, now the function always drops non-mapping loci). o Implemented getIslandStatus(), getProbeType(), getSnpInfo() and addSnpInfo(). The two later functions retrieve pre-computed SNP overlaps, and the new annotation object includes SNPs based on dbSNP 137, 135 and 132. o Changed the IlluminaMethylatioAnnotation class to now include genomeBuild information as well as defaults. o Added estimateCellCounts for deconvolution of cell types in whole blood. Thanks to Andrew Jaffe and Andres Houseman. Changes in version 1.5: o Added unit testing for the preprocessing algorithms. o Improved the speed of SWAN for large datasets. o Added the new class "GenomicRatioSet". It is akin to "GenomicMethylSet" but instead of containing Meth and Unmeth it contains M and/or Beta and copy number. o We now depend on illuminaio instead of crlmm in order to get readIDAT. o Added unsrturl.bst to minimize dependences for running Sweave. Changes in version 1.3: o Updated preprocessSwan to fix a bug when mSet was not set to the default value of NULL. Specifically, now the "counts" tables is used to construct "subset". o Changed the function manifestNew() to IlluminaMethylationManifest(). o Added IlluminaMethylationAnnotation(). o Added placeholders for unit testing based on RUnit. o Introduced a new show method for MethylSet and RGChannelSet, derived from the eSet method in Biobase. o The annotation slot of a MethylSet/RGChannelSet is now intended to _not_ be a scalar, but instead have length 2 with components 'array' and 'annotation'. This foreshadows introdution of annotation packages for use with minfi. o Reorganization of R files; rewriting of the man pages for MethylSet, RGChannelSet. o getMeth, getUnmeth, getBeta, getM are now methods. o bug fix to qcReport thanks to Tao Shi. o Changes to getBeta / getM, both in terms of which arguments the methods take and how the values are computed. o Changes to the manifest structure; it now has separate slots for genotype probes and these probes are no longer part of a MethylSet (using eg. preprocessRaw). They can be accessed using getProbeInfo(rgSet, type) with type equal to "SnpI" or "SnpII". o Introduction of mapToGenome, getLocations and the new class GenomicMethylSet. man pages are reasonably complete, still need to add examples to the vignette. This will be a standard part of an extended pipeline. o Introduction of IlluminaHumanMethylation450lannotation.ilmn.v1.2 which contains some new annotation needed for mapToGenome/getLocations. This package will be split into several packages moving forward, in an attempt to harmonize efforts by us and Tim Triche. getLocations/mapToGenome will stay the same. o getControlTypes added (returns the different types of control probes). o GenomicMethylSet now inherits a number of methods including granges(), start(), end() etc. from SummarizedExperiemnt. They have therefore been deleted from minfi. o Bugfix to getLocations(..., mergeManifest = TRUE). It now longer throws an error. o mapToGenome now returns a GenomicMethylSet ordered according to the chromosome name ordering chr1,..,chr22,chrX,chrY,unmapped, the last one not present if drop=TRUE (default). Changes in version 1.1: o Changed NAMESPACE file o Defined constructors for MethylSet, RGChannelSet, RGChannelSetExtended. o Included a version number in the class definition for MethylSet and RGChannelSet. Old objects can be updated by calls of the form updateObject(Mset). o read.manifest (not exported) updated to include nCpGs. o preprocessSwan was added. Still work in progress. o Changed background calculation in preprocessSwan. o Added a section to the vignette describing preprocessSwan. o Bug fix: ilogit2 is now in base (it used to be base e). Thanks to Time Triche, Jr . o Added and dcoumented the IlluminaMethylationAnnotation class; still work in progess. o Moved package vignette from inst/doc to vignettes. Changes in version 0.99: o Initial release to Bioconductor. o Added NEWS file. o Bugfix to vignette. o readIDAT is now exported by crlmm, implying that we can import this function through NAMESPACE.