2009-03-01 Benilton Carvalho - committed version 1.0.40 * Added TODO file * Added CHANGES file * Reduced number of files in R/ by combining functions for a given methodology (crlmm / cnrma) * Files with suffix XYZ-functions.R should have *functions* for methodology XYZ * Files with suffix XYZ-methods.R should have *methods* for methodology XYZ * Imported assayDataNew from Biobase * Added inst/scripts to store vignettes that can't be built by BioC due to the fact that they depend on external data not available as BioC data packages * Added crlmmSet class and calls/confs methods 2009-03-08 Benilton Carvalho - committed version 1.0.55 * Added biocViews * Removed empty \details{} in cnrma.Rd 2009-03-14 Benilton Carvalho - committed version 1.0.56 * Loaded data in cnrma-functions.R to an environment and extracted from there so we can get rid of the NOTES complaining about 'no visible bindings'. 2009-03-18 Rob Scharpf - committed version 1.0.57 * Added steps object to instantiateObjects to speed up debugging * Reformulated the regression for chromosome X - estimate cross-hybridization using chromosome X * Take into account pseudo-autosomal regions on chr X for copy number estimation * Replaced get() and assign() with '<-' operations to improve readability * Function to compute posterior means of copy number estimates 2009-03-19 Rob Scharpf - committed version 1.0.59 * Requires genomewidesnp6Crlmm version 1.0.1 or greater 2009-03-25 Rob Scharpf - committed version 1.0.60 * simplified some of the preliminary steps for the computeCopynumber function * crlmm output subset within the body of the function * modified vignette -- store results in an oligoSnpSet object (for now) * added function to extract the date from the celfile headers (celDates) 2009-03-25 Rob Scharpf - committed version 1.0.61 * update to copynumber vignette 2009-03-27 B Carvalho - committed version 1.0.62 * crlmm() returns a SnpSet object (from Biobase) * fixed standard vignette to accommodate this change * redefined calls/confs to accommodate this change * fixed documentation to acommodate this change 2009-03-28 B Carvalho - committed version 1.0.64 * modified crlmm and cnrma to look for data at extdata/ 2009-03-29 Rob Scharpf - committed version 1.0.65 * update to copynumber vignette * updated computeCopynumber.Rd to accommodate SnpSet objects and changes to genomewidesnp6Crlmm * cnrma function requires the cdfName * update man files for cnrma and computeCopynumber 2009-03-30 Matt Ritchie - committed version 1.0.66 * added functions to read in idat files, pre-process and genotype data from Illumina SNP arrays (functions named readIdatFiles() and crlmmIllumina() in crlmm-illumina.R) * added man pages for these functions 2009-04-01 Matt Ritchie - committed version 1.0.67 * added import statement for normalize.quantiles 2009-04-01 R.Scharpf - committed version 1.0.69 * added a few items to the crlmm TODOs 2009-04-03 B Carvalho - committed version 1.0.70 * Updated TODO and DESCRIPTION 2009-04-04 R.Scharpf - committed version 1.0.71 * bug in oneBatch function for chromosome X. added additional checks for missing values 2009-04-06 Matt Ritchie - committed version 1.0.72 * new argument in readIdatFiles() 'saveDate', which saves the date and time each array is decoded and scanned * results from crlmmIllumina() now saved as 'SnpSet' just like crlmm() * reorganised Illumina preprocessing functions slightly to - allow copy number intensities to be saved along with snp intensities - make use of new indexing objects in the chip specific crlmm data packages - fix a few bugs 2009-04-07 Rob Scharpf - committed version 1.0.73 * added cdfName as argument to computeCopynumber 2009-04-07 B Carvalho - committed version 1.0.74 * Added documentation for snprma. * Removed 'svn:executable' property of readIdatFiles.Rd 2009-04-07 Rob Scharpf - committed version 1.0.75 * modifications to chromosome X copy number estimation 2009-04-07 Rob Scharpf - committed version 1.0.76 * fixed bug in cnrma 2009-04-07 Rob Scharpf - committed version 1.0.77 * cnrma accepts other cdfNames * fixed bug in cnrma 2009-04-07 Rob Scharpf - committed version 1.0.78 * added conf as argument to instantiateObjects 2009-04-08 Matt Ritchie - committed version 1.0.79 * fixed bug in readIDAT and readIdatFiles from reading in RunInfo header information 2009-04-07 B Carvalho - committed version 1.0.80 (advantages of being a lot of hours behind) * Fixed downstream vignette to account for the SnpSet object being returned by crlmm * Fixed some minor status messages 2009-04-09 R Scharpf - committed version 1.0.81 * added a skeleton of a copy number vignette for the illumina platform (illumina_copynumber.Rnw) to inst/scripts 2009-04-27 R Scharpf - committed version 1.3.1 * Fixed bug in nonpolymorphic() function 2009-05-07 Matt Ritchie - committed version 1.3.2 * Updated usage of sampleNames() on NChannelSet objects in Illumina functions to maintain consistency with Biobase 2009-06-08 B Carvalho - committed version 1.3.3 * Added batchQC to phenoData 2009-06-08 R Scharpf - committed version 1.3.4 * fixed bug in the biasAdjNP function. updated biasAdj function 2009-06-20 R Scharpf - committed version 1.3.5 * created CrlmmSetList, ABset, and CopyNumberSet classes. - added a few methods to support these classes * crlmmWrapper does normalization / genotyping and optionally splits the results by chromosome * several changes to the copynumber vignette 2009-06-29 R Scharpf - committed version 1.3.6 * updated computeCopynumber * export A, B methods for ABset class 2009-07-01 M Ritchie - committed version 1.3.7 * made memory savings to reading and normalization of Illumina data * Now use 'protocolData' slot to save scan dates instead of saving them in phenoData slot * added vignette for genoytping illumina data (crlmmIllumina.pdf in inst/doc and crlmmIllumina.Rnw in inst/scripts) * Changed stop() to warning() when idats are of different type in readIdatFiles() 2009-07-06 R Scharpf - committed version 1.3.8 * initial development of copy number methods for illumina platform * added Rd files for previously defined classes/methods * some improvements to chromosome X copy number estimation 2009-07-06 R Scharpf - committed version 1.3.9 * fixed bugs in biasAdj and biasAdjNP 2009-07-09 R Scharpf - committed version 1.3.10 * changed defaults for crlmmWrapper: save.it=FALSE * splitByChr method looks for 'chr' or 'chromosome' in colnames * sample-specific standard deviations in the .getEmission function * add check for duplicated positions in creating locusset object * computeCopynumber returns an object of class CrlmmSetList - dimnames for the elements in the list are the same - elements in the list are ordered by chromosome and physical position - copy number parameters in the featureData of the CopyNumberSet element are thresholded 2009-07-14 R Scharpf - committed version 1.3.11 * computeCopynumber requires 10 or more samples 2009-07-16 R Scharpf - committed version 1.3.12 * protocolData replacement method for CrlmmSetList objects * added .man page for .computeCopynumber * Suggests VanillaICE (>= 1.7.8) -- needed to run the copynumber.Rnw vignette 2009-07-16 R Scharpf - committed version 1.3.13 * fixed bug 'DF.PRIOR not found' 2009-07-16 R Scharpf - committed version 1.3.14 * fixed malformed DESCRIPTION file 2009-07-31 B Carvalho - committed version 1.3.16 * Removed several warnings at the C-level * Fixed several incorrect links in the documentation * Removed multiple notes "no visible binding for global variable" by replacing, in crlmmIlluminaWrapper and crlmmWrapper, a) samplesheet5 by get("samplesheet5") b) path by get("path") c) res by get("res") 2009-08-04 R. Scharpf - committed version 1.3.17 * changed readIdatFiles function to check whether arrayNames is NULL 2009-08-13 R. Scharpf - committed version 1.3.18 * move Biobase to Depends * removed GGdata from suggests (problem with loading illuminaHumanv1.db) * overhaul of vignette * added update() method for copy number * added documentation and error checks for crlmmWrapper 2009-08-14 R. Scharpf - committed version 1.3.19 * changes to crlmmWrapper (trying to make this handle the illumina platform as well...still needs testing) - removed crlmmIlluminaWrapper.Rd, and commented crlmmIlluminaWrapper function * labeled figures / displayed output of code chunks in the copy number vignette * added bibliography for copy number vignette. Added file inst/doc/refs.bib * added boxplot method 2009-10-03 R. Scharpf - committed version 1.3.21 * modified crlmmWrapper function * modified illumina copy number vignette (still needs debugging) * changed title of copy number vignette * added reference to the crlmm paper * changed copyNumber() method so that CA + NA = NA, CB + NA = NA (previously had CA+NA=CA, but this can result in a lot of zeros, depending on the genotype) * new method: addFeatureAnnotation * support for snp5.0 2009-10-04 R. Scharpf - committed version 1.3.22 * changed default path argument for readIdatFiles to empty quotes * fixed bug in update method for character strings * updated addFeatureAnnotation so that CHR arg not required * fixed bug in nonpolymorphic function -- function checks whether any regions are pseudoautosomal * fixed bug in list2locusset function (no longer assigns genomewidesnp6 as the default annotation) 2009-10-16 R. Scharpf - committed version 1.3.23 * 100*CA, 100*CB are stored in the CA, CB assayDataElements. The replacement method automatically converts a matrix on the copy number scale to an integer representation by scaling by a factor of 100. The accessor methods for CA, CB automatically divide by 100 to return estimates back on the original copy number scale. * more debugging of readIdatFiles and illumina copy number vignette. * updated illumina_copynumber vignette 2009-10-25 M Ritchie - committed version 1.3.24 * fixed bug in readIdatFiles() * updated crlmmIllumina.Rnw and crlmmIllumina.pdf 2009-11-14 B Carvalho - committed version 1.5.2 * code cleanup - removed unneeded C code 2009-11-15 R. Scharpf - committed version 1.5.3 * numerous changes to the copy number estimation - ABset and CrlmmSetList classes are gone. Using SnpCallSetPlus and CrlmmSet - Added class SegmentSet that extends CrlmmSet directly. 2009-11-15 B Carvalho - committed version 1.5.4 * removed references to old C code * added the missing files to the Collate field * fixed classes imported from oligoClasses in NAMESPACE * imported 'calls<-' from oligoClasses 2009-11-19 R. Scharpf - committed version 1.5.5 * removed a few of the classes (CrlmmSet, CrlmmSetFF, SnpCallSetPlusFF,...) * added CNSet class * segmentData slot in CNSet class is an extension of RangedData (defined in IRanges package) 2009-11-19 R. Scharpf - committed version 1.5.6 * fixed bugs in initialization of SnpCallSetPlus 2009-11-19 R. Scharpf - committed version 1.5.7 * fixed bugs in addFeatureAnnotation.SnpCallSetPlus 2009-12-01 M. Ritchie - committed version 1.5.8 * bug fixed in stripNormalize() [X+16,Y+16 which avoids log(0) = -Inf values, removed inadvertantly in version 1.3.7, put back] * removed header checking from readIdatFiles() (seems to fail often). Instead check that the number of SNPs agrees (to within +/- 10K SNPs) 2009-12-04 B. Carvalho - committed version 1.5.11 * moved IRanges and oligoClasses to Depends (DESCRIPTION) 2009-12-23 R. Scharpf - committed version 1.5.17 ** updated first half of inst/scripts/copynumber.Rnw, as well as a few of the help files 2009-12-23 R. Scharpf - committed version 1.5.18 ** removed generics for addFeatureAnnotation and GT<- 2009-12-24 M. Ritchie - committed version 1.5.19 * Added 'humanomni1quadv1b" to chip types allowed in RGtoXY() 2010-01-20 R. Scharpf - committed version 1.5.21 * Added CopyNumberVariants to DESCRIPTION 2010-01-20 R. Scharpf - committed version 1.5.22 * restored inst/doc/crlmmDownstream.Rnw 2010-02-04 M. Ritchie - committed version 1.5.23 * crlmmIllumina now exported in NAMESPACE (removed at some point) * new function crlmmIlluminaV2() which reads in .idats and genotypes in the one function to reduce memory usage (not exported as yet) * readIdatFiles() modified to no longer store number of beads and beads SE to save memory. Instead, 'zero', which indicates which SNPs have zero beads is stored in the assayData slot. * now store 'zero' with copy number AB intensities in preprocessInfinium2() * deleted man pages crlmm.Rd and readIdatFiles.Rd added back 2010-02-05 M. Ritchie - committed version 1.5.24 * preprocessed allele A and B intensities from copy number and regular SNPs are now saved separately by crlmmIllumina(). The 'intensityFile' argument has been replaced by 'snpFile' and 'cnFile'. * updated the following man pages to reflect the above changes and added in current references: crlmmIllumina.Rd, crlmm.Rd and readIdatFiles.Rd 2010-02-07 B. Carvalho - committed version 1.5.25 * Updated requirement of affyio to support Win64 2010-02-20 R. Scharpf - committed version 1.5.26 ** begin adding support for ff ** added use.poe option for nonpolymorphic loci ** crlmm does not return anything, but saves the following objects: - genotypes.rda - confs.rda - snp_rmaResult.rda (gns, sns, SNR, SKW, mixtureParams, cdfName) - A.rda - B.rda - cn_rmaResult.rda (SKW) 2010-02-21 R. Scharpf - committed version 1.5.27 ** additional support for ff in crlmm and computeCopynumber functions 2010-03-02 M. Ritchie - committed version 1.5.28 * Added message to readIDAT() warning that older style IDAT files can not be read in. Such files arise when scanner settings contain the line false If this is modified to true, then readIDAT() should work. Thanks to Pierre Cherel who reported this error. * Removed AllClasses.R from Collate field in DESCRIPTION file (causes an error in build) 2010-03-05 M. Ritchie - committed version 1.5.29 * crlmmIlluminaV2() now exported. Added man page crlmmIlluminaV2.Rd 2010-03-07 R. Scharpf committed version 1.5.30 - one can use ff in conjunction with affy platforms 5.0 and 6.0 - preprocessing / genotyping is basically the same set of commands with either illumina/affy platforms (though illumina-users may have to play with some of the options for reading idat files - if ff package is loaded, the assayData elements are ff objects - the classes all inherit from 'CrlmmContainer' that contains an additional slot 'options' and 'genomeAnnotation'. options is a list with the default arguments to snprma, crlmm, etc, as well as a few global settings such as 'verbose' and 'seed'. I added the genomeAnnotation slot simply because I want to be able to use ff-objects for the feature-level data. Maybe with setClassUnion we could avoid adding the genomeAnnotation slot (and use featureData instead), but I didn't have much success with this. - the batchSize argument will run the genotyping (crlmmGT) in batches to reduce the RAM. The default is batches of size 1000. - The crlmm.Rd file contains an example with / without ff for Affymetrix data. 2010-03-08 M. Ritchie committed version 1.5.31 * removed a few unnecessary lines of code from crlmm-illumina.R (zero not needed as argument for preprocessInfinium2() and storageMode should not be "lockedEnvironment" in RGtoXY()) * added "humanomni1quadv1b" to validCdfName() in utils.R 2010-03-08 R.Scharpf committed version 1.5.32 ** Rolled back to version 1.5.24 2010-03-08 R.Scharpf committed version 1.5.33 ** Added annotatedDataFrameFrom methods for ff_matrix and ffdf (in utils) 2010-03-10 R.Scharpf committed version 1.5.34 ** updated DESCRIPTION to import ff ** added AllClasses.R with defitions for ff-derived classes ** temporarily exporting everything in the NAMESPACE 2010-03-11 R.Scharpf committed version 1.5.35 ** added genotype() in cnrma-functions -- for preprocessing and genotyping affy 2010-03-14 R.Scharpf committed version 1.5.36 ** added crlmmIlluminaRS to cnrma-functions.R (testing) 2010-03-18 R.Scharpf committed version 1.5.37 ** fixed bugs in genotype() and crlmmIlluminaRS. (currently saving intermediate steps in crlmmIlluminaRS) removed cnOptions function and changed arguments to crlmmCopynumber 2010-03-18 R.Scharpf committed version 1.5.38 ** a few updates to initializeBigMatrix ** show, [ defined for CNSetLM 2010-03-25 R.Scharpf committed version 1.5.41 ** import snpCall, snpCallProbability, snpCall<-, snpCallProbability<- from Biobase ** updates to genotype, crlmmIlluminaRS, crlmmCopynumber ** class union of ff_matrix, matrix, and ffdf 2010-03-18 B Carvalho committed version 1.5.42 ** added parallel/large dataset support to snprma/crlmm ** merged changes on .41 with my local changes 2010-04-01 R.Scharpf committed version 1.5.44 ** added functions genotype2, cnrma2 for preprocessing and genotyping with crlmm2 ** added crlmmCopynumber2 for parallel support with copy number est. (needs more checking) 2010-04-07 M. Ritchie committed version 1.5.45 ** modified the storage of RG, XY and genotype call data to use the ff package and initializeBigMatrix() function from oligoClasses package. The genotype call data now includes non-polymorphic probes (which have NA calls). Functions which use ff storage are named readIdatFiles2(), RGtoXY2(), preprocessInfinium2v2(), crlmmIllumina2() and crlmmIlluminaV2(). 2010-04-08 B Carvalho committed version 1.5.46 ** moved NEWS to inst/ 2010-04-09 M. Ritchie committed version 1.5.47 ** fixed bugs in code and removed copy number probes from output (now saved separately as before - SnpSuperSet not used) ** crlmmIllumina2() and crlmmIlluminaV2() now use the crlmmGT2() function (which expects ff objects and supports parallel processing) ** updated crlmmIllumina.pdf vignette 2010-04-11 R. Scharpf committed version 1.5.48 ** added a few .Rd files 2010-04-16 B Carvalho committed version 1.5.49 ** cosmetics - looking for cause of memory spike 2010-05-26 R Scharpf committed version 1.6.1 ** added sample CNSetLM object ** fixed inst/scripts/copynumber.pdf vignette ** fixed inst/scripts/illumina_copynumber.pdf vignette 2010-05-26 R Scharpf committed version 1.6.2 ** fixed bug in copyNumber method for CNSet 2010-06-19 R Scharpf committed version 1.6.3 ** modified construct() function so that the phenoData is created before initializing a CNSetLM object. Exposed a few helper functions in the crlmm_illumina vignette