### 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
