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 if Illumina data
* Now use 'scanDates' 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()
