2009-03-01  Benilton Carvalho <bcarvalh@jhsph.edu> - 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 <bcarvalh@jhsph.edu> - committed version 1.0.55
 
 * Added biocViews
 
 * Removed empty \details{} in cnrma.Rd

 
 2009-03-14 Benilton Carvalho <bcarvalh@jhsph.edu> - 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 <rscharpf@jhsph.edu> - 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 <GenerateVersionTwoIdatFiles>false</GenerateVersionTwoIdatFiles>
 If this is modified to <GenerateVersionTwoIdatFiles>true</GenerateVersionTwoIdatFiles>, 
 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

 2010-04-24 B Carvalho committed version 1.7.1
 ** fixed bug in gender prediction that cause a spike in memory usage

 2010-05-25 R. Scharpf committed version 1.7.2
 ** added example dataset
 ** fixed vignette: inst/scripts/copynumber.Rnw

 
 2010-05-25 R. Scharpf committed version 1.7.3
 ** put back in the following check in readIDAT (from r 45050):
   if(versionNumber<3)
     stop("Older style IDAT files not supported:  consider updating your scanner settings")
 
 2010-05-25 R. Scharpf committed version 1.7.4
 ** wrapped readIDAT in a tryCatch()	   

 
 2010-05-26 R. Scharpf committed version 1.7.5
 ** minor edits to inst/scripts/copynumber.Rnw

 
 2010-07-25 M. Ritchie committed version 1.7.6
 ** fixed bug introduced in 1.7.4 by addition of tryCatch() into readIdatFiles().  Thanks to Nolwenn Le Meur for pointing this out.

 
 2010--7-28 M. Ritchie committed version 1.7.7
 ** added omni express 12 as one of the chip options for Illumina.  Also added a check for copy number probes (this chip doesn't have any).

 
 2010-07-30 R. Scharpf 1.7.8

 ** edited construct function for CNSetLM
 
 2010-08-25 M. Ritchie 1.7.12
 ** Renamed functions readIdatFiles2() -> readIdatFiles(), RGtoXY2() -> RGtoXY(), preprocessInfinium2v2() -> preprocessInfinium2(), crlmmIllumina2() -> crlmmIllumina().  These make use of ff objects to store data.
 ** Exported crlmmIlluminaV2(), which combines reading in of idats and genotyping in one.  Also added a man page for this function

 ** Added close() statements to readIdatFiles(), RGtoXY() and stripNormalize().  Added open() statement to stripNormalize(). Moved close() statement in preprocessInfinium2()

 ** tidied up crlmm-illumina.R, removing commented out code.

 2010-09-16 M. Ritchie 1.7.14

 ** added immuno chip 12 as one of the chip options for Illumina.
 

 2010-09-28 M. Ritchie 1.7.15
 ** added functions get.ProtocolData.Illumina(), construct.Illumina() and genotype.Illumina() to maintiain consistency with Rob's Affy functions
 ** removed 'save.it', 'load.it', 'snpFile', 'cnFile' arguments from crlmmIllumina(), crlmmIlluminaV2 and preprocessInfinium2().  Updated man pages to reflect these changes.
 ** added a switch so that both regular matrix/ff storage can be handled in each function, depending upon whether the ff package has been loaded.

 
 2010-09-30 M. Ritchie 1.7.16
 ** copy number A and B intensities now stored in callSet from genotype.Illumina()

 2010-10-06 M. Ritchie 1.7.19

 ** new internal function processIDAT which uses ocLapply() to parallelize pre-processing of Illumina data
 ** changes to genotype.Illumina()

 ** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf

 
 2010-10-07 M. Ritchie 1.7.20
 ** updated vignettes - crlmmIllumina.Rnw and crlmmIllumina.pdf
 ** tidied code and added snp.index to ffrowapply() in genotype.Illumina() when calls and confidence values are being updated in callSet.

 
 2010-10-11 M. Ritchie 1.7.21
 ** fixed bug with indexes for ffrowapply() in genotype.Illumina()
 

 2010-10-17 M. Ritchie 1.7.22
 **  added "humanomni25quadv1b" to validCdfName() in utils.R and RGtoXY() in crlmm-illumina.R