| cghRA-news | R Documentation |
Manual page cleanup.
Vignette addition.
Non-base package functions are now properly identified, to comply with R CMD check.
C entry points are now registered, to comply with R CMD check.
'states' argument default values harmonized across the package.
cghRA.copies$newSTEPS() replaces cghRA.copies$STEPS().
Better rendering for plots in tk.modelize() for Linux and/or R >= 3.4.0.
Better automatic sizing of the plot in tk.browse().
cghRA.copies$STEPS() no longer crashes if 'nested' is not 'none' with an empty region table.
tk.series() rebuilt, moving some elements to the new tk.annotate().
White image at tk.modelize() start.
segmentMap class added for cnvScore maps.
cghMCR algorithm no longer available in cghRA.series.
GADA segmentation no longer available in cghRA.array.
cghRA.copies$segMerge() removed as conflicting with Rgb::track.table.
process.replicates() no longer crashes when no duplicated probe is present.
cnvScore(), map2design(), applyMap() and trace2track() added.
"dgv.track" dataset and track.CNV.DGVsupp() added.
chromEnd argument added to STEPS(), default behavior changed from TRUE to FALSE.
newSTEPS() added, as a function and cghRA.series method.
cghRA.array class code reformated.
cghRA.array$chromosomes() added.
NAMESPACE and dependencies updated to comply with new R policies.
cghRA.series$show() fixed for empty series.
cghRA.series$pool() now accepts a 'group' argument.
cghRA.series$pool() now complies with Rgb::track.CNV types.
'cluster' argument from process() modified, see the manual page.
cghRA.series$SRA(), $LRA() and $STEPS() now produce tracks based on Rgb::draw.steps().
process() rewritten for more flexibility.
cghRA.copies, cghRA.regions and cghRA.probes packages merged into cghRA.
segMerge() and UTILS.tk removed, as already defined in package Rgb.
IRanges package dependency in localize() replaced by Rgb.
process() can now be launched without log file.
DNAcopy bug temporarly fixed in cghRA.array$DNAcopy().
"CBS default" added to process.default() for 'segmentArgs'.
'quiet' argument added to cghRA.series$pool().
Agilent.design() now relies on cghRA.design() constructor.
'colorFun' defaults for cghRA.regions and cghRA.copies redefined to comply with Rgb 1.0.0.
cghRA.series$applyMethod() no longer crashes with methods returning NULL.
cghRA.series$pool() now relies on Rgb::track.CNV class.
track.lone occurences renammed in track.table, for Rgb compatibility.
cghRA.copies now relies on its model's ploidy for default drawing origin.
cghRA.copies no longer enforces a new default parameter for colorFun.
Error in cghRA.series$pool() fixed.
cghRA.probes now inherits from refTable, no more from track.part.
cghRA.probes now have its own 'name' field, no more inherited.
cghRA.array now inherits an independant 'name' field from the drawable class, no more linked to its 'probes' 'name' field.
cghRA.array$initialize() and cghRA.array$defaultParams() updated to current Rgb standards (0.5.0).
cghRA.array$maskByFlag() no longer raises error about data class.
cghRA.array$replicates() no longer raises error about data class.
parseKaryo() argument 'alteratedOnly' added, with a new default (previous behavior was like 'FALSE').
parseKaryo() now returns a list with an additional clone summary.
parseKaryo() added.
cghRA.series$MCR() renammed into cghRA.series$STEPS().
'mode' argument added to cghRA.regions$proportions().
defParam() overloads replaced by defaultParams() overloads.
Dependency 'cghRA.track' becomes 'Rgb'.
Tk windows names and titles fixed on Gnome 3.
Icons replaced by 16x16 and 32x32 GIF images.
Tk style 'clam' is the new default on unix platforms.
Tk file selection windows become transients.
process.one() timers in logs fixed on unix platforms.
X11 warnings silenced in tk.file() to fix 'X11 BadDrawable'.
'karyotype' method moved from cghRA.array class to cghRA.regions.
'mergeArms' and 'splitArms' renamed into 'eraseArms' and 'addArms' to avoid confusion.
cghRA.series constructor now accepts RDT file path vectors.
Agilent.design() now uses R NA values for 'NA.[number]' probe names.
'chrom' argument related systematic error corrected in cghRA.array$GLAD().
process() 'do...' arguments merged in a single 'steps' argument.
process() 'output' argument replaced by 'outputDir'.
process() 'fun' argument replaced by 'replicateFun'.
process() 'replicateFun' type changed from function name to function.
'Spatial' checkbox added to tk.process().
process.one() no longer takes its arguments in the global environnement.
Profiles added in tk.process().
process.default() added.
cghRA.copies class added.
cghRA.regions$model.apply() no longer alter itself, but return a cghRA.copies object.
getParameters() overloads replaced by defParam() overloads for the package classes.
'maxElements' and 'label' default parameters added to cghRA.design class.
Drawing parameters pre-set in cghRA.array$pool() track output.
cghRA.array$pool() unified to use 'states' and 'values' rather than 'keep'.
'Pool' track production added to tk.series().
cghRA.array also implements getChromEnd() for optimisation.
cghRA.regions$proportions() added.
'segMerge' method added to cghRA.regions class.
TK file choosing windows now remind last directory browsed.
require() calls turned into library() ones to raise errors.
GLAD segmentation and calling added to cghRA.array class.
draw() overloads replaced by getParameters() overloads for the package classes.
cghRA.regions$status() rebuilt from ground to mimic cghRA.regions::penetrance behavior.
cghRA.series$pool() added.
process() now accepts other Probe file parsers than Agilent.probes.
process() 'column' argument removed, 'arrayFiles' replaced by 'probeFiles', 'probeParser' and 'probeArgs' added.
process() and tk.process() arguments 'filePattern' and 'fileReplace' removed.
process() now ignore 'spatial' step if 'row' and 'col' are not available.
tk.process() 'probeParser' argument added.
tk.process() 'fillGaps' argument is no longer checked by default, as the MCR algorithm can handle it.
Agilent.probes() 'name' argument removed.
Segmentation 'min.width' default value switched back to DNAcopy default (2 presently) in tk.process().
'Keep all segmentations' behavior added to tk.process(), process() and process.one().
'exclude' argument definition added to tk.process().
tk.design() know produces '*.design.rdt' files, for smarter file selection.
'index' field and buildIndex methods added to track.lone class, to fulfill cghRA.track::subtrack 1.0.5 updates.
tk.series() MCR now produces a 'boundariesProbeCount' column.
'tracks' argument added to parallelize, penetrance, MCR, SRA and LRA methods for cghRA.series.
'Penalty' replaced by 'Allow nested' in tk.series().
cghRA.series$hasState method replaced by cghRA.regions$status.
cghRA.series$applyMethod .mode argument added, to control output type.
cghRA.series$applyMethod nrow relies on 'arrays' names rather than 'name' for faster computation.
Cytoband file selection added in tk.design().
'...' was not passed through by cghRA.regions$fillGaps.
'utils', 'stats', 'graphics' and 'grDevices' were not loaded on cluster members in process.one().
Extra vertical space deplaced from top to bottom in tk.series().
tk.cghRA() window name changed to 'cghRA - Data processor'.
'blocking' argument added to tk.cghRA(), for stand alone version.
'strand' column added to pass cghRA.regions$check() in tk.series().
Error message reshaping in tk.design().
Error message reshaping in process.one().
'doFittest' was not exported from process() to process.one().
'No fittest segmentation found' warning added to process.one().
'fittest' section added to process.one() log file.
Default 'nperm' in tk.process() changed to 25/alpha.