R News


rCGH package 1.1.7
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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 package.


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


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


rCGH package 1.1.4
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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 package 1.1.3
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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 package 1.1.2
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BUG FIXES
    * Major bug fixed in the view() function: one function was not properly
    called.



rCGH package 1.1.1
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Not submitted!



rCGH package 1.1.0
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New bioconductor devel versioning after release cycle.
The first and corresponding bioconductor release version is 1.0.0.



rCGH package 0.99.10
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BUG FIXES
    * In view() function: segment colors were not properly assigned.



rCGH package 0.99.9
-----------------------

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



rCGH package 0.99.8
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BUG FIXES
	* Error when merging probes with duplicated locations on
    Agilent CytoGenomics 3.0: fixed.



rCGH package 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 package 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 package 0.99.5
-----------------------

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



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

SIGNIFICANT USER-VISIBLE CHANGES
    * No changes

NEW FEATURES
    * New package

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