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


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()