CHANGES
f32a09dd
 2009-03-01  Benilton Carvalho <bcarvalh@jhsph.edu> - committed version 1.0.40
3620e6b1
 
 * 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
f32a09dd
 
07cc385e
 * Imported assayDataNew from Biobase
f32a09dd
 
 * 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
07cc385e
 
 2009-03-08 Benilton Carvalho <bcarvalh@jhsph.edu> - committed version 1.0.55
 
 * Added biocViews
 
 * Removed empty \details{} in cnrma.Rd
c027cd73
 
 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'.
f8af2fff
 
 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
cfdeb14b
 * crlmm output subset within the body of the function
f8af2fff
 * modified vignette -- store results in an oligoSnpSet object (for now)
 * added function to extract the date from the celfile headers (celDates)
 
001bc9f5
 2009-03-25 Rob Scharpf - committed version 1.0.61
 * update to copynumber vignette
 
95d22b50
 2009-03-27 B Carvalho - committed version 1.0.62
f8af2fff
 
95d22b50
 * crlmm() returns a SnpSet object (from Biobase)
f8af2fff
 
95d22b50
 * fixed standard vignette to accommodate this change
f8af2fff
 
95d22b50
 * redefined calls/confs to accommodate this change
f8af2fff
 
95d22b50
 * fixed documentation to acommodate this change
ec428e7e
 
67e99be3
 2009-03-28 B Carvalho - committed version 1.0.64
5dab0fa8
 * modified crlmm and cnrma to look for data at extdata/
ec428e7e
 
5dab0fa8
 2009-03-29 Rob Scharpf - committed version 1.0.65
67e99be3
 
5dab0fa8
 * 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
cd8b85b6
 
 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
 
58b6a5dc
 2009-04-01 Matt Ritchie - committed version 1.0.67
 
 * added import statement for normalize.quantiles
e446e21d
 
 2009-04-01 R.Scharpf - committed version 1.0.69
 
 * added a few items to the crlmm TODOs
cd3930b6
 
 2009-04-03 B Carvalho - committed version 1.0.70
 
cfdeb14b
 * Updated TODO and DESCRIPTION
a83b4acf
 
 2009-04-04 R.Scharpf - committed version 1.0.71
 
 *  bug in oneBatch function for chromosome X.  added additional checks for missing values
cfdeb14b
 
 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
07882625
 
 2009-04-07 Rob Scharpf - committed version 1.0.73
 
 * added cdfName as argument to computeCopynumber
268a6dce
 
b938db26
 2009-04-07 B Carvalho - committed version 1.0.74
268a6dce
 
 * Added documentation for snprma.
 
 * Removed 'svn:executable' property of readIdatFiles.Rd
eafb5d9b
 
b938db26
 2009-04-07 Rob Scharpf - committed version 1.0.75
eafb5d9b
 
 * modifications to chromosome X copy number estimation
 
b938db26
 2009-04-07 Rob Scharpf - committed version 1.0.76
b84929f4
 
 * fixed bug in cnrma
 
b938db26
 2009-04-07 Rob Scharpf - committed version 1.0.77
fc48b56e
 
 * cnrma accepts other cdfNames
 
 * fixed bug in cnrma
 
b938db26
 2009-04-07 Rob Scharpf - committed version 1.0.78
467ebfda
 
 * added conf as argument to instantiateObjects
 
b938db26
 2009-04-08 Matt Ritchie - committed version 1.0.79
467ebfda
 
b938db26
 * fixed bug in readIDAT and readIdatFiles from reading in RunInfo header information
b5bb7de9
 
 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
e19041ae
 
 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
eb2aa777
 
 2009-04-27 R Scharpf - committed version 1.3.1
 
 * Fixed bug in nonpolymorphic() function
9564b5c5
 
 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
685829f7
 
 2009-06-08 B Carvalho - committed version 1.3.3
 
 * Added batchQC to phenoData
a6a2c12f
 
 2009-06-08 R Scharpf - committed version 1.3.4
 
 * fixed bug in the biasAdjNP function.  updated biasAdj function
38fb1b80
 
 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
 
45dab54b
 2009-06-29 R Scharpf - committed version 1.3.6
38fb1b80
 
45dab54b
 * updated computeCopynumber
 * export A, B methods for ABset class
38fb1b80
 
852cc5cf
 2009-07-01 M Ritchie - committed version 1.3.7
 
a24cf336
 * made memory savings to reading and normalization of Illumina data
4b098e36
 * Now use 'protocolData' slot to save scan dates instead of saving them in phenoData slot
852cc5cf
 * 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()
38fb1b80
 
64463948
 
 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
 
923a155c
 2009-07-06 R Scharpf - committed version 1.3.9
 
 * fixed bugs in biasAdj and biasAdjNP
 
b9c71726
 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
 
9a0ac5c0
 2009-07-14 R Scharpf - committed version 1.3.11
 
 * computeCopynumber requires 10 or more samples
 
b9c71726
 
c336dedf
 2009-07-16 R Scharpf - committed version 1.3.12
 
4b098e36
 * protocolData replacement method for CrlmmSetList objects
c336dedf
 
 * added .man page for .computeCopynumber 
 
529394e3
 * 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'
c336dedf
 
99c5e1e2
 2009-07-16 R Scharpf - committed version 1.3.14
 
 * fixed malformed DESCRIPTION file
 
f9b19c6c
 2009-07-31 B Carvalho - committed version 1.3.16
c336dedf
 
f9b19c6c
 * 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")
fe3e3f61
 
 2009-08-04 R. Scharpf - committed version 1.3.17
 
 * changed readIdatFiles function to check whether arrayNames is NULL
43b13ec9
 
 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
bd722b7c
 
 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 
2ae7850e
 
 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
e4e0b214
 
 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)
3ddde61b
 
 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
 
d3a7556e
 2009-10-25 M Ritchie - committed version 1.3.24
3ddde61b
 
d3a7556e
  * fixed bug in readIdatFiles()
3ddde61b
 
d3a7556e
  * updated crlmmIllumina.Rnw and crlmmIllumina.pdf
10632b3f
 
 2009-11-14 B Carvalho - committed version 1.5.2
 
  * code cleanup - removed unneeded C code
bf8acd05
 
 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.
 
8bbb1b13
 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
bf8acd05
 
96d10c6e
 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)
 
12ef4585
 2009-11-19 R. Scharpf - committed version 1.5.6 
89ff1833
 
12ef4585
  * fixed bugs in initialization of SnpCallSetPlus
 
 2009-11-19 R. Scharpf - committed version 1.5.7
 
  * fixed bugs in addFeatureAnnotation.SnpCallSetPlus
89ff1833
 
3407f177
 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]
8499df94
  * removed header checking from readIdatFiles() (seems to fail often).  
       Instead check that the number of SNPs agrees (to within +/- 10K SNPs)
824cfde4
 
 2009-12-04 B. Carvalho - committed version 1.5.11
 
  * moved IRanges and oligoClasses to Depends (DESCRIPTION)
7ae22f52
 
a24cf336
 2009-12-23 R. Scharpf - committed version 1.5.17
7ae22f52
 
 ** updated first half of inst/scripts/copynumber.Rnw, as well as a few of the help files
73436da1
 
a24cf336
 2009-12-23 R. Scharpf - committed version 1.5.18
73436da1
 
 ** removed generics for addFeatureAnnotation and GT<-
 
a24cf336
 2009-12-24 M. Ritchie - committed version 1.5.19
 
  * Added 'humanomni1quadv1b" to chip types allowed in RGtoXY()
8f4e2eab
 
 2010-01-20 R. Scharpf - committed version 1.5.21
  * Added CopyNumberVariants to DESCRIPTION
26b9b406
 
 2010-01-20 R. Scharpf - committed version 1.5.22
  * restored inst/doc/crlmmDownstream.Rnw
4e4601af
 
 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()
33bc8e1b
  * deleted man pages crlmm.Rd and readIdatFiles.Rd added back
3462bc81
 
 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'.
33bc8e1b
  * updated the following man pages to reflect the above changes and added in current references:  crlmmIllumina.Rd, crlmm.Rd and readIdatFiles.Rd
e24f3a23
 
 2010-02-07 B. Carvalho - committed version 1.5.25
  * Updated requirement of affyio to support Win64
7e1d14dd
 
2ebe94e0
 2010-02-20 R. Scharpf - committed version 1.5.26
7e1d14dd
 
 ** 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)
 
2ebe94e0
 2010-02-21 R. Scharpf - committed version 1.5.27
b7a8abf0
  
 ** additional support for ff in crlmm and computeCopynumber functions
 
2ebe94e0
 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)
6b85c46e
 
 2010-03-05 M. Ritchie - committed version 1.5.29
  * crlmmIlluminaV2() now exported.  Added man page crlmmIlluminaV2.Rd
a13f66d1
 
 2010-03-07 R. Scharpf committed version 1.5.30
 
e1909d6b
        - 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.
b32471ae
 
 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
5fcfed7d
 
 2010-03-08 R.Scharpf committed version 1.5.32
 
e1909d6b
 **	   Rolled back to version 1.5.24 
5fcfed7d
 	   
a4ece851
 2010-03-08 R.Scharpf committed version 1.5.33
5fcfed7d
 
a4ece851
 **	  Added annotatedDataFrameFrom methods for ff_matrix and ffdf (in utils)
a3335242
 
 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
e1909d6b
 
 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)
 
1c2a3f47
 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
 
fd653332
 2010-03-18 R.Scharpf committed version 1.5.38
 
 ** a few updates to initializeBigMatrix
 ** show, [ defined for CNSetLM
afb508f9
 
c00f715a
 2010-03-25 R.Scharpf committed version 1.5.41
afb508f9
 
 ** import snpCall, snpCallProbability, snpCall<-, snpCallProbability<-
    from Biobase
c00f715a
 ** updates to genotype, crlmmIlluminaRS, crlmmCopynumber
afb508f9
 ** class union of ff_matrix, matrix, and ffdf
c00f715a
 
f0da6921
 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
d5bc779e
 
 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)
e609f78b
 
 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().
61043805
 
 2010-04-08 B Carvalho committed version 1.5.46
 ** moved NEWS to inst/
a11efc9c
 
 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
ea66649b
 
 2010-04-11 R. Scharpf committed version 1.5.48
 ** added a few .Rd files
 
551018e8
 2010-04-16 B Carvalho committed version 1.5.49
 ** cosmetics - looking for cause of memory spike
ea66649b
 
d41653db
 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
 
dbee8270
 2010-06-19 R Scharpf committed version 1.6.3
 
 ** modified construct() function so that the phenoData is created
863d2e2b
    before initializing a CNSetLM object.  Exposed a few helper
    functions in the crlmm_illumina vignette
dbee8270
 
ea66649b