[BioC] minfi release 1.8

Elmar Tobi e.tobi at lumc.nl
Thu Nov 14 08:45:04 CET 2013

Really Cool Kasper,
Many thanks for the excellent programming and lots of work.

Op woensdag 13 november 2013 01:12:46 UTC+1 schreef Kasper Hansen:

> 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 <gba... at gmail.com<javascript:>
> >).
>     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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