As part of Bioconductor 2.13, we have released minfi 1.8.x.  Due to a
number of last minute errors, the recommended version is 1.8.3 (or bigger).

Users may find that their old objects cannot be linked to annotation.
 Please run
 OBJECT = updateObject(OBJECT)
to fix this.

Highlights include
* preprocessingQuantile(): an independent implementation of the same ideas
as in Tost et al.
* bumphunter() for finding DMRs
* blockFinder() for finding large hypo-methylated blocks on the 450k array.
* estimateCellCounts() for estimating cell type composition for whole blood
samples. The function can be extended to work on other types of cells,
provided suitable flow sorted data is available.
* the annotation now includes SNP annotation for dbSNP v132, 135 and 137,
independently annotated at JHU.
* getSex(): you can now get sex repeatedly, irrespective of relationship
status.
* minfiQC: find and remove outlier samples based on a sample QC criteria we
have found effective.

Unfortunately, none of these handy changes are yet detailed in the
vignette; we are working on this.

A manuscript is in review detailing most of these functions.

Full NEWS below

Best,
Kasper D Hansen

    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 <gbayon@gmail.com>).

    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.

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