CHANGES

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

2010-11-18 M. Ritchie 1.9.8
** genotype.Illumina() is now exported and has a man page.  The argument 'outdir' should 
be used to specify where you want to store the large data objects.  ldPath(outdir) is specified 
inside preprocessInfinium2()
** the 'batch' variable is now left empty and must be specified by the user
** X and Y are now initialized with zeroes by initializeBigMatrix( ,initdata=0) in RGtoXY().
** open(A(callSet); open(B(callSet) replaces open(callSet) in genotype.Illumina()

2010-12-10 M. Ritchie 1.9.9
** ffcolapply() now used instead of ffrowapply()
** ff storage only used to initialize callSet - no longer used in storage of RG, XY, res data created along the way (matrices now used here) etc.
** removed 'outdir' argument and ldPath() added in 1.9.8
** verbose argument added to readIdatFiles()