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()
