[BioC] minfi release 1.8
Elmar Tobi
e.tobi at lumc.nl
Mon Dec 9 17:16:39 CET 2013
Dear Kasper:
it returns: "IlluminaHumanMethylation450k"
Which is indeed a golden oldie...
best,
Elmar
Op maandag 9 december 2013 16:43:29 UTC+1 schreef Kasper Hansen:
>
> This should work, but I am unsure why it doesn't. You may have a very old
> object. Could you send me the output of
>
> RGset.7 at annotation
>
> In the meantime, you should be able to do this by essentially grabbing the
> slot from minfiData, ie.
>
> library(minfiData)
> data(RGsetEx)
> RGset.7 at annotation = RGsetEx at annotation
>
> and then check
> validObject(RGset.7)
> (which should return TRUE).
>
> Best,
> Kasper
>
>
>
>
>
> On Mon, Dec 9, 2013 at 10:30 AM, Elmar Tobi <e.t... at lumc.nl <javascript:>>wrote:
>
>> Dear Kasper,
>>
>>
>> For older objects I have been trying to update the annotation to
>> IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
>> But I am getting an error:
>>
>> RGset.c <- updateObject(RGset.7)
>>
>> "Error in if (object at annotation["annotation"] == "ilmn.v1.2")
>> object at annotation["annotation"] <- .default.450k.annotation :
>> missing value where TRUE/FALSE needed"
>>
>>
>> The RGset is a plain one:
>>
>> RGset.7
>> "RGChannelSet (storageMode: lockedEnvironment)
>> assayData: 622399 features, 605 samples
>> element names: Green, Red
>> phenoData
>> sampleNames: 7310440029_R05C01 7310440029_R05C02 ...
>> 7497398051_R02C01 (605 total)
>> varLabels: hofnum labnr ... v050 (41 total)
>> varMetadata: labelDescription
>> Annotation
>> *array: IlluminaHumanMethylation450k"*
>>
>>
>> (Running on R 3.0.2 with minfi 1.8.8).
>>
>> Do you have any idea on how to update?
>>
>> Best wishes
>>
>>
>>
>>
>>
>>
>> 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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>
>
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