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Bioconductor Changlog.
Tue, 13 Oct 2009
tilingArray
fixed an unnecessary restriction in function 'normalizeByReference' that had prevented it from working with matrices of less than 200,000 rows
tilingArray
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
tilingArray
minor, cosmetic update to plotSegmentationHeatmap
tilingArray
Removed unneeded geneplotter dependency.
tilingArray
Standardizing reference to Artistic License 2.0.
tilingArray
fixed minor bug in function plotAlongChrom that occurred when no region coordinates were supplied, i.e. one wanted to plot the data for the whole chromosome, with an environment of segmenation objects.
tilingArray
I reran segmentation.Rnw and made an up-to-date segmentation.pdf
(nothing substantial has changed, but the vignette and the software
needed testing after introduction of NAMESPACE.)
tilingArray
I changed the code assessNorm.Rnw to use Biostrings functions, rather than the old matchprobes stuff.
Added dependency of the segmentation.Rnw vignette on geneplotter (as that package is now longer automatically attached with the
tilingArray package) and re-made the PDF.
tilingArray
Added package dependencies in the vignettes
inst/scripts/assessNorm.Rnw and inst/scripts/segmentation.Rnw that
used to be attached automatically (but are no longer)
Removed an extraneous "browser" from R/confint.segmentation.R
Added a call to library(vsn) to inst/scripts/assessNorm.Rnw since
vsn is no longer attached when tilingArray is loaded (due to use of
NAMESPACE / Imports).
tilingArray
Adapted segChrom to also work with Ringo's probeAnno class;
some documtation improvements.
tilingArray
I adapted the vignettes to the fact that use of NAMESPACE now requires explicit loading of some packages they use.
I rerean assessNorm.pdf. segmentation.pdf still needs to be done.
tilingArray
fixed a minor bug in function 'plotSegmentationHeatmap' that resulted in segmentation lines being drawn at the wrong position if the supplied x-coordinates are the genomic START postions of probe matches instead of their mid positions
tilingArray
Removed redundant code from .onAttach()
tilingArray
Added "Rplots.pdf" to the "clean" target of Makefile
tilingArray
Now Zhenyu is the maintainer!
tilingArray
Nicer implementation of the "matrix_length" functionality.
Fixed typo: was 'maxcp', now 'maxseg'.
Better treatment of integer overflow in determination of allocVector's length
argument for when space for two matrices is allocated (v1, v2 in function
'findsegments_dp'). See also my today's mail on the mailing list.
Precisified the "Title" field in DESCRIPTION.
tilingArray
moved set.seed to the beginning of the vignette 'findsegments' to make introductory simple example reproducible as well
tilingArray
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
tilingArray
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
tilingArray
I updated the man page for normalizeByReference, to make clear
that it calls vsnMatrix for between array normalisation.
I also changed lots of Dependencies into Imports.
tilingArray
removed quotes from do.call