Any tutorial on how to remove probes that contains SNPs? On Tuesday, November 12, 2013 7:12:46 PM UTC-5, Kasper Hansen wrote: > > 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. >