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
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
