R News


rCGH 1.3.4
-----------------------
Major changes
    * EMnormalize() has a new 'priorScale' argument (default to 5) to optimize 
    the gaussian mixture analysis and the identification of the major L2Ratio
    peaks.

NEW FEATURES
    * The rCGH package now supports Affymetrix OncoScan arrays. As for SNP6.0
    and CytoScan arrays, CEL files must be processed by the user first, using
    either ChAS or Affymetrix Power Tools. See ?readAffyOncoScan for more
    details.


rCGH 1.1.8 has been released as rCGH-1.2.2
-----------------------

rCGH 1.1.8
-----------------------
Major changes
    * The centralization is now estimated on the distribution of segment values,
    so after the segmentation step. This mean that now users have to run
    segmentCGH() before EMnormalize().

NEW FEATURES
    * plotProfile() gains a 'showCopy' argument. When set to 'TRUE', the
    profile's y-axis will use the estimated copy numbers instead of the
    Log2Ratios.

    * The read() functions, used as rCGH-Object constructors, take a
    supplementary 'ploidy' argument. When known, this value can be used in order
    to estimate gains and losses expressed in copy numbers. Default to 2.

    * Copy number estimation is also reported in all of the tables, inlcuding
    the main by-probe table accesible through getCNset().


rCGH 1.1.7
-----------------------
NEW FEATURES
    * The user can now specify what supplementary genes annotations to export
    through the byGeneTable() function. Allowed annotations are those supported
    by the 'select' method from the 'AnnotationDbi' bioconductor.


rCGH 1.1.6
-----------------------
BUG FIXES
    * Errors occured when mergin short segments, with respect to the minLen
    argument in segmentCGH().


rCGH 1.1.5
-----------------------
Cleaner version from 1.1.4.
Should not give any warning due to functions masked by imported packages


rCGH 1.1.4
-----------------------
NEW FEATURES
    * Read Illumina HumanOmniExpress: this function has been temporarily
    removed. Illumina data require to much memory for annotating probes when
    probe locations are missing in the data.


rCGH 1.1.3
-----------------------

NEW FEATURES
    * Read Illumina HumanOmniExpress: see readIllumina() help in the rCGH
    documentation.
    * New rCGH-generic class for custom arrays: see readGeneric() help in the
    rCGH documentation.
    * Supports arrays designed according to hg18, hg19 (default) and hg38. To be
    specified by the user in the read functions and in the byGeneTable function.
    * plotProfile now as pCol and GLcol arguments, for points and gained/lost
    segments, respectively.



rCGH 1.1.2
-----------------------

BUG FIXES
    * Major bug fixed in the view() function: one function was not properly
    called.



rCGH 1.1.1
-----------------------

Not submitted!



rCGH 1.1.0
-----------------------

New bioconductor devel versioning after release cycle.
The first and corresponding bioconductor release version is 1.0.0.



rCGH 0.99.10
-----------------------

BUG FIXES
    * In view() function: segment colors were not properly assigned.



rCGH 0.99.9
-----------------------

BUG FIXES
    * In view() function: segment colors were not properly assigned.



rCGH 0.99.8
-----------------------

BUG FIXES
	* Error when merging probes with duplicated locations on
    Agilent CytoGenomics 3.0: fixed.



rCGH 0.99.7
-----------------------

SIGNIFICANT USER-VISIBLE CHANGES
    * byGeneTable() is not a S4 method anymore but S3: as argument, it takes a
    segmentation table exported from a rCGH object, and not the object itself.
    As a consequence, byGeneTable() can be used on any segmentation table of the
    same form as those exported from a rCGH object.

    * The full by-gene table is not stored in rCGH object, but built then
    exported on the fly, using byGeneTable().
    
    * Supplementary argument in getSegTable(): minLen allows the user to
    specify the minimal segment length, in Kb. Segments shorter than this value
    are merged before the segmentation table is exported. The original table is
    still stored in the rCGH object.
    
    * New features in plotProfile() and multiplot(): one or multiple genes can
    be tagged. As for getSegTable(), the minimal segment length (in Kb) can be
    specified.

    * Server version for the interactive viewer is described in the vignette.

BUG FIXES
    * byGeneTable:
        . In the exported by-gene table, the corresponding segment lengths were
        not properly reported.

        . Errors occured when a gene was covered by 2 segments.


rCGH 0.99.6
-----------------------

SIGNIFICANT USER-VISIBLE CHANGES
    * New cytoScan example file
    * Updated vignette
    * The rCGH version used is stored in rCGH objects for traceability

NON-VISIBLE CHANGES
	* Supplementary unittests



rCGH 0.99.5
-----------------------

SIGNIFICANT USER-VISIBLE CHANGES
    * R-3.2.1 is the minimal required version



rCGH 0.99.4: First release!
-----------------------

SIGNIFICANT USER-VISIBLE CHANGES
    * No changes

NEW FEATURES
    * New

BUG FIXES
    * No changes classified as 'bug fixes'  under active development)
