v1.43.1 Tightened the recognition code for 27k data to avoid conflict with the next release of the Allergy and Asthma array.
v1.39.1 Initial support for the Allergy and Asthma array.
v1.39.2 More support for the Allergy and Asthma array.
v1.39.3 Bug fix that prevented R CMD build from working.
v1.29.4 Fixed a bug in detectionP where the function
always returned NA for a 27k array. Reported by Laurenz Holcik.
v1.29.4 Fixed a bug in preprocessNoob where the
function would error when supplied an input data set with only 1
sample (when using default arguments). Reported by Matt Oldach.
v1.27.2 Fix bug in preprocessQuantile() that arose when
checking input for previous preprocessing method. Thanks to @DelnazR for
the report (https://github.com/hansenlab/minfi/issues/165).
v1.27.3 Fixed bug related to switch A and B for SNPs of type I when using convertArray / combineArrays. Reported by Jenny van Dongen.
v1.27.3 Fixed error in dmpFinder.
Added preliminary support for HorvathMammalMethylChip40.
v1.26.1: dmpFinder() again works when dat is
a numeric matrix. This bug was introduced in v1.26.0 during the
transition to support DelayedArray-backed minfi objects. Thanks to
@ralowe for the report (#163).
Changed default annotation for EPIC arrays to B4 from B2.
Added preliminary support for DelayedArray-backed minfi objects. This allows disk-backed minfi objects (e.g., using HDF5). This functionality is currently recommended only for developers and advanced users. A user-friendly interface is currently in development. All existing minfi functionality and serialized objects should continue to work as it did in versions prior to 1.25. Please report any problems to the GitHub issue tracker.
Fixing bug in functions readGEORawFile() and getGenomicRatioSetFromGEO(). These two functions did not work (reported an error). They should work now. Thanks to users who reported problems at GitHub issues.
Updated CITATION and citations in the vignette.
Fixed as() (coercion) from RGChannelSetExtended to RGChannelSet, to support the argument extended=TRUE in read.matharray(). The core issue is the new("RChannelSetExtended") is an invalid object because it does not have correct elements of the assay slot. Instead of addressing this, I used a check for ncol=0, nrow=0 in the coercion function which asssumes the presence of correctly named assays. Original issue report by Stewart Morris <[email protected]>.
Improved (made prettier) the printing of messages in read.metharray() and friends.
Changed seqlevels(..., force = TRUE) to seqlevel(..., pruning.mode = "coarse").
Moving RGChannelSet, MethylSet and RatioSet from building on eSet (from Biobase) to SummarizedExperiment (from SummarizedExperiment). Most important changes are that the constructor functions now uses the argument colData instead of pData; some of them have more arguments. The updateObject methods have been extended to update to the new class backend. While the pData, sampleNames, featureNames methods still work, we recommend (at least for package writers) to move to colData, colnames and rownames.
Reverted the bugfix to preprocessQuantile mentioned under news for version 1.19. Our fix was wrong; the original code did not have a bug. Thanks to users who reported issues with the function (Frederic Fournier and David Martino).
bugfix for getSnpBeta for subsetted (and combined) RGChannelSets (reported and diagnosed by Warren Cheung).
Accessing the manifest or annotation now fails for an 'unknown' array.
We now support gzipped IDAT files.
Fixed a bug in read.metharray() which resulted in an error in some situations when running the function with argument force=TRUE to read IDAT files of different length. Reported by Maria Calleja Cervantes <[email protected]>.
preprocessNoob gets a dyeMethod argument which now allows for true single sample processing.
combineArrayTypes is added; the intention is to be able to combine 450k and EPIC array data at the RGChannelSet level.
Support for early access IDAT files form the EPIC array.
message() is now used instead of cat().
Some functions moved from deprecated to defunct.
Addressing a bug in preprocessQuantile which led to reduced performance for Type I probes when run with default paramters (stratified=TRUE). Users are strongly encouraged to update to the latest version (1.19.7 or greater) and rerun the function.
Extended combineArrayTypes to deal with control probes with the same address, but different characteristics (Color, Type, ExtendedType). Discussions with Illumina support reveals that, for control probes, same address is same probe.
Extended combineArrayTypes to support [Genomic](Methyl|Ratio)Set.
Fixed a bug that made detectionP fail with an error if used on only 1 sample.
Fixed a bug in read.metharray where we assumed a certain ordering is consistent in IDAT files from different samples. This is no longer assumed, but as a consequence the function is a bit slower. Bug (indirectly) observed by Giovanni Calice <[email protected]>.
Changing internals of MethylSet() to follow recent changes in assayDataElement<- in Biobase 2.33.1.
Changing internals of MethylSet() (again) to follow recent changes in assayDataElement<- in Biobase 2.33.2.
Fixing issues with combine() on various classes where pData columns doesn't have the same class. This translates to fixes for combineArrays and estimateCellType.
estimateCellCounts gets a referencePlatform array (defaulting to 450k) and now silently converts the input data to the desired platform using convertArray.
Major refactoring of the annotation packages to reduce memory consumption.
Adding testing for preprocessNoob, preprocessFunnorm.
Fxing some verbose output of preprocessNoob.
Adding non-exported function .digestVector for testing.
read.450k.exp has support for argument base when targets is supplied. Thanks to Brent Pedersen <[email protected]> for noticing this and providing an initial fix.
changed the default behaviour of read.450k.exp. If called using a targets argument created by read.450k.sheet, you should not also give it a base argument (which was always superfluous).
Some NAMESPACE imports fixes.
getGenomicRatioSetFromGEO added to read directly from GEO and create a GenomicsRatioSet. Thanks Tim Triche for writing the original function.
makeGenomicRatioSetFromMatrix added. This function turns a matrix into a GenomicRatioSet. The 450K feature IDs need to be supplied or in the rownames of the matrix.
makeGenomicRatioSetFromMatrix added to convert matrices to GenomicRatioSets. This can be useful for reading in files with beta values and turning into object that can be directly passed to bumphunter and blockFinder.
readGEORawFile added to read raw intensity files provided as Supplementary Material on GEO. The files include the unmethylated and methylated signals. The new function returns a GenomicMethylSet which permits you to seamlessly apply minfi preprocessing functions.
readTCGA is wrapper for makeGenomicRatioSetFromMatrix that reads in files in the TCGA format. The function is very specific to this format.
Minor coding fixes including some NAMESPACE issues, missing pData<- methods, replace require() with requireNamespace().
cpgCollapse now works for GenomicRatioSets since it no longer attempts to summarize CN data when passed a GenomicRatioSet.
estimateCellCounts now works on only 2 cell types.
Various NAMESPACE fixes.
the gaphunter function by Shan Andrews has been added. We welcome Shan as a contributing author.
Updated CITATION.
Added dropLociWithSnps for easy exclusion of certain methylation loci.
Add getAnnotationObject for easy printing of contents of the annotation object.
Changes in 1.10 imported into 1.11.
Fixed an issue with bumphunter calling the bumphunter package in a wrong way.
Added getOOB and getSnpBeta convenience functions for accessing the OOB probes and the SNP probes.
read.450k.sheet now forces a column named Slide to be character.
The NOOB background correction method is now available throguh preprocessNoob.
One can now supply the permutations to be used in permutation analysis. This is useful for cases in which the total number of possilbe permutations is small and one wants to use them all or in cases in which one wants to assure balance, for example, between cases and controls.
The bumphunter method now has the option to create null distributions using a bootstrap approach.
Fixed a man page issue.
Added GitHub URL to DESCRIPTION.
Functional normalization now supports background correction by NOOB (see preprocessNoob); this is recommended (and the new default).
Modified read.450k.sheet to ignore case when identifying the data header "[DATA]". This addresses an issue with sheets generated by some Illumina instruments. Reported and partial fix provided by the github user nilsigem.
Importing the changes from 1.8 into 1.9.
Added the withColor argument to the getProbeType function, which allows the return of "IGrn", "IRed", "II", instead of only "I", "II".
Added asList argument to getControlAddress to return result as a list.
Moved reshape from Depends to Imports.
Dramatic improvement in memory usage of preprocessRaw.
Updated CITATION, the minif paper is in press.
Fixed bug with mapToGenome(..., mergeManifest = TRUE) reported by Dale Watkins <[email protected]> and Allegra A. Petti <[email protected]>.
Fixed bug with mapToGenome(rSet) with rSet being a RatioSet with the CN set to NULL reported byAllegra A. Petti <[email protected]>.
Added preprocessFunnorm, a new preprocessing method.
Improvements to the speed of getAnnotation by Martin Morgan <[email protected]>.
preprocessQuantile(object) would fail if object was a GenomicMethylSet. This is now fixed.
Cleanup of Rd markdown in various help files.
estimateCellCounts would throw an error. This is now fixed. The function arguments have changed.
Bug in cpgCollapse led to incorrect results. Your output is affected if table(granges(output[[1]])$type) is all 'OpenSea'. Reported by Florence Cavalli <[email protected]>.
Encapsulated the example for estimateCellCounts() in 'dontrun', to disable it on the build servers.
preprocessQuantile would work as if removeBadSamples=TRUE no matter the value of the argument.
Fixing replace bug in fixMethOutliers; it would not work on the output of preprocessSWAN. Reported by David McGaughey <[email protected]>.
The function mapToGenome would return something that looked like an unordered GenomicMethylSet. Actually, loci were correctly ordered within chromosomes, the issue had to do with whether the chromosomes were ordered as chr1, chr2, chr3 (used in minfi) or chr1, chr10, chr11 (lexigraphically). Reported by Florence Cavalli <[email protected]>.
Switched to using new author format in DESCRIPTION.
Added getMethSignal(), a convenience function for programming.
Changed the argument name of "type" to "what" for getMethSignal().
Added the class "RatioSet", like "GenomicRatioSet" but without the genome information.
Bugfixes to the "GenomicRatioSet()" constructor.
Added the method ratioConvert(), for converting a "MethylSet" to a "RatioSet" or a "GenomicMethylSet" to a "GenomicRatioSet".
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 <[email protected]>).
Added fixMethOutliers for thresholding extreme observations in the [un]methylation channels.
Added getSex, addSex, plotSex for estimating sex of the samples.
Added getQC, addQC, plotQC for a very simple quality control measure.
Added minfiQC for a one-stop function for quality control measures.
Changed some verbose=TRUE output in various functions.
Added preprocessQuantile.
Added bumphunter method for "GenomicRatioSet".
Handling signed zero in minfi:::.digestMatrix which caused unit tests to fail on Windows.
addSex and addQC lead to sampleNames() being dropped because of a likely bug in cbind(DataFrame, DataFrame). Work-around has been implemented.
Re-ran the test data generator.
Fixed some Depends and Imports issues revealed by new features of R CMD check.
Added blockFinder and cpgCollapse.
(internal) added convenience functions for argument checking.
Exposed and re-wrote getAnnotation().
Changed getLocations() from being a method to a simple function. Arguments have been removed (for example, now the function always drops non-mapping loci).
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.
Changed the IlluminaMethylatioAnnotation class to now include genomeBuild information as well as defaults.
Added estimateCellCounts for deconvolution of cell types in whole blood. Thanks to Andrew Jaffe and Andres Houseman.
Added unit testing for the preprocessing algorithms.
Improved the speed of SWAN for large datasets.
Added the new class "GenomicRatioSet". It is akin to "GenomicMethylSet" but instead of containing Meth and Unmeth it contains M and/or Beta and copy number.
We now depend on illuminaio instead of crlmm in order to get readIDAT.
Added unsrturl.bst to minimize dependences for running Sweave.
Updated preprocessSwan to fix a bug when mSet was not set to the default value of NULL. Specifically, now the "counts" tables is used to construct "subset".
Changed the function manifestNew() to IlluminaMethylationManifest().
Added IlluminaMethylationAnnotation().
Added placeholders for unit testing based on RUnit.
Introduced a new show method for MethylSet and RGChannelSet, derived from the eSet method in Biobase.
The annotation slot of a MethylSet/RGChannelSet is now intended to _not_ be a scalar, but instead have length 2 with components 'array' and 'annotation'. This foreshadows introdution of annotation packages for use with minfi.
Reorganization of R files; rewriting of the man pages for MethylSet, RGChannelSet.
getMeth, getUnmeth, getBeta, getM are now methods.
bug fix to qcReport thanks to Tao Shi.
Changes to getBeta / getM, both in terms of which arguments the methods take and how the values are computed.
Changes to the manifest structure; it now has separate slots for genotype probes and these probes are no longer part of a MethylSet (using eg. preprocessRaw). They can be accessed using getProbeInfo(rgSet, type) with type equal to "SnpI" or "SnpII".
Introduction of mapToGenome, getLocations and the new class GenomicMethylSet. man pages are reasonably complete, still need to add examples to the vignette. This will be a standard part of an extended pipeline.
Introduction of IlluminaHumanMethylation450lannotation.ilmn.v1.2 which contains some new annotation needed for mapToGenome/getLocations. This package will be split into several packages moving forward, in an attempt to harmonize efforts by us and Tim Triche. getLocations/mapToGenome will stay the same.
getControlTypes added (returns the different types of control probes).
GenomicMethylSet now inherits a number of methods including granges(), start(), end() etc. from SummarizedExperiemnt. They have therefore been deleted from minfi.
Bugfix to getLocations(..., mergeManifest = TRUE). It now longer throws an error.
mapToGenome now returns a GenomicMethylSet ordered according to the chromosome name ordering chr1,..,chr22,chrX,chrY,unmapped, the last one not present if drop=TRUE (default).
Changed NAMESPACE file
Defined constructors for MethylSet, RGChannelSet, RGChannelSetExtended.
Included a version number in the class definition for MethylSet and RGChannelSet. Old objects can be updated by calls of the form updateObject(Mset).
read.manifest (not exported) updated to include nCpGs.
preprocessSwan was added. Still work in progress.
Changed background calculation in preprocessSwan.
Added a section to the vignette describing preprocessSwan.
Bug fix: ilogit2 is now in base (it used to be base e). Thanks to Time Triche, Jr <[email protected]>.
Added and dcoumented the IlluminaMethylationAnnotation class; still work in progess.
Moved package vignette from inst/doc to vignettes.
Initial release to Bioconductor.
Added NEWS file.
Bugfix to vignette.
readIDAT is now exported by crlmm, implying that we can import this function through NAMESPACE.