[BioC] minfi release 1.8
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
> * 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
> 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
> 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
> 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
> 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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