### CHANGE log for package oligoClasses ###
Changes made by Matt Settles 12-4-2008
** All changes should generally have effect on only Affy Tiling, ST and expression arrays.
added classes AffyExonPDInfo and AffySTPDInfo
03-09-09 - Benilton Carvalho - committed version 1.5.6
** Small changes to reduce duplication of code for Gene and Exon Affymetrix arrays.
03-11-09 - Benilton Carvalho - committed version 1.5.7
** Added accessors for Affy Tiling arrays.
03-17-09 - Benilton Carvalho - committed version 1.5.11
** Generalized bg/bgindex methods for FeatureSet objects.
03-18-09 - Benilton Carvalho - committed version 1.5.12
** Fixed all warnings so it passes CHECK.
03-20-09 - R. Scharpf - committed version 1.5.14
** Removed requirement that chromosome be stored as a character string in oligoSnpSet featureData slot
** Removed calculateCopyNumber.Rd file
03-23-09 - R. Scharpf - committed version 1.5.15
** Removed requirement that chromosome be stored as a character string in SnpCallSet and SnpCopyNumberSet
03-24-09 - B Carvalho - committed version 1.5.16
** Removed unused TilingQSet-class
** Redefined sampleNames method for FeatureSet-like objects so it returns a vector. Because I changed FeatureSet (it now contains "NChannelSet" instead of "eSet"), sampleNames() would return a list (on "NChannelSet", elements of assayData are allowed to have different colnames). For the applications I foresee oligo being used, this (different colnames) should not be the case...
** Changed definition of FeatureSet. Instead of 'eSet', it contains "NChannelSet".
** Added TilingFeatureSet2 class, with two channels, to accommodate 2-colors applications of Tiling arrays.
03-25-2009 - B Carvalho
** Changes to accommodate sequence methods
** Added slot annotation to PDInfo, so we can easily find any information about the object.
03-25-2009 - B Carvalho
** Removed lots of unneeded things from NAMESPACE
** Implemented better definitions in NAMESPACE
** Fixed problem with sampleNames dispatching a warning.
04-07-2009 - R Scharpf committed v1.5.19
** Removed chromosome requirement in setValidity for oligoSnpSet, SnpCallSet, and SnpCopyNumberSet
04-07-2009 - R Scharpf committed v1.5.20
** Changed initialization method for oligoSnpSet and SnpCopyNumberSet
04-16-2009 - B Bcarvalho committed v 1.5.23
** Cleaned up code
05-07-2009 - B Bcarvalho committed v 1.7.1
** Cleaned up code
06-19-2009 - B Carvalho committed v 1.7.5
** Fixed mmSequence
07-17-2009 - B Carvalho committed v 1.7.7
** Extended pmChr to TilingFeatureSet2
07-25-2009 - B Carvalho committed v 1.7.9
** Removed annotation from show method
08-05-2009 - B Carvalho committed v 1.7.10
** Added automatic downloarder/installer pdPkgFromBioC()/requireAnnotation() to be used with annotation packages
** Added requireAnnotation, which is pretty much require() if the pkg is installed... and installs it, without asking, ortherwise.
08-06-2009 - B Carvalho committed v 1.7.10
** For the moment, I don't think pdPkgFromBioC/requireAnnotation need to be exposed in NAMESPACE
09-01-2009 - B Carvalho committed v 1.7.12
** requireAnnotation back in NAMESPACE
09-01-2009 - B Carvalho committed v 1.7.13
** bgindex now sorted
09-27-2009 - B Carvalho committed v 1.7.15
** added documentation to pdPkgFromBioC and requireAnnotation
09-29-2009 - B Carvalho committed v 1.7.16
** svn add documentation
10-28-2009 - R. Scharpf committed v 1.9.1
** export TilingFeatureSet2, QuantificationSet
11-19-2009 - R. Scharpf committed v 1.9.2
** changed definition of SnpCallSetPlus extends SnpSet and SnpQSet
12-01-2009 - R. Scharpf committed v 1.9.7
** removed SnpLevelSet
** oligoSnpSet extends SnpSet
12-02-2009 - B. Carvalho committed v 1.9.9
** moved several methods to oligo
** trying to keepp only accessors and replace methods in oligoClasses
** exposing callsConfidence - until it comes from Biobase
12-10-2009 - B. Carvalho committed v 1.9.15
** added intensityFile slot to FeatureSet class, it'll be NA for regular
use and the filename (full) for persistent storage
12-19-2009 - R. Scharpf committed v 1.9.17
** added man pages for AlleleSet, SnpSuperSet, and CNSet
12-20-2009 - R. Scharpf committed v 1.9.19
** removed SnpLevelClasses Vignette and supporting documents in inst/doc
** added man/Snp-methods.Rd
** added man/list.cefiles.Rd
12-23-2009 - R. Scharpf committed v 1.9.21
** removed IRanges dependency. Added a few .Rd files. Note IRanges
is still loaded because of Biostrings dependency on IRanges. Do we
need Biostrings?
12-30-2009 - R. Scharpf committed v 1.9.22
** removed segmentData from initialization method for CNSet objects
01-23-2010 - B. Carvalho committed v 1.9.25
** exported bothStrands()
01-28-2010 - B. Carvalho committed v 1.9.26
** changed confs() slightly to agree with oligo
02-07-2010 - B. Carvalho (1.9.27)
** Updated requirement on affyio so Win64 is supported
02-20-2010 - R. Scharpf (1.9.28)
** Added CopyNumberSet class as a container for total copy number with
no slots for genotypes. (Mainly for use with VanillaICE)
** Defined methods for db, chromosome, position, and isSnp at the
level of eSet (formerly, these were defined at the SnpSet level). I
did this so that CopyNumberSet, which extends eSet directly, could
inherit these methods
02-20-2010 - R. Scharpf (1.9.29)
** modified initialization method for SnpSet. I would have preferred
to modify the initialization in VanillaICE, but I had problems with
this
02-20-2010 - R. Scharpf (1.9.30)
** moved A, B accessors from crlmm to oligoClasses. Updated a few of the man pages.
** added oligoClasses.Rnw vignette
03-04-2010 - B Carvalho (1.9.32)
** exposed DBPDInfo, ExpressionPDInfo, FeatureSet, TilingPDInfo
** fixed NEWS file
03-10-2010 - R.Scharpf (1.9.35)
** export A<-, B<- for AlleleSet
03-10-2010 - B Carvalho (1.9.37)
** adding ff utilities to be used in oligo and crlmm
** adding tools to diagnose cluster/large dataset support
** (1.9.39) fixed broken export and added p2i/i2p functions to simplify future changes on the conversion
** (1.9.40) fixed oligoProbeset/oligoSamples to be ocProbesets/ocSamples
** (1.9.41) fixed unload / docs
03-20-2010 - B Carvalho (1.9.44)
** fixed bugs that broke oligo::crlmm (initialization method for AlleleSet and getM/getA)
03-22-2010 - B Carvalho (1.9.45)
** add some docs
** commented out example (CNSet) the breaks completely the build process
** added eval=FALSE on the vignette on the relevant part so the pkg can be built
** fixed initialization for CNSet to conform changes on 1.9.44.
03-22-2010 - B Carvalho (1.9.46)
** fixed is.ffmatrix example
** fixed alias for allele
03-31-2010 - B Carvalho (1.9.50)
** moved initializeBigMatrix and initializeBigVector from crlmm to oligoClasses
03-31-2010 - R. Scharpf (1.9.51)
** added a few Rd files
04-03-2010 - R. Scharpf (1.9.52)
** added a few Rd files
04-04-2010 - R. Scharpf (1.9.53)
** addFeatureAnnotation.crlmm provides a warning rather than perform a
subset operation on the eSet object. Subset operations are
dangerous with ff objects
04-08-2010 - B Carvalho (1.9.54)
** moved NEWS to inst/
04-10-2010 - B Carvalho (1.9.55)
** initializeBig(Vector/Matrix) get a 'initdata' argument
05-22-2010 - R. Scharpf (1.11.1)
** fixed man page for requireClusterPkgSet. Added integerScoreToProbability function.
06-30-2010 - R. Scharpf (1.11.2)
** added checkExists utility to oligoClasses package
(checks objects in workspace or specified file directory before executing a function)
10-29-2010 - B Carvalho (1.13.2)
** removed man/flags.rda
