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 '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