Entering edit mode
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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