Changes in version 1.19.4:
o CHANGE: As the bigmemory package is not available for Windows, only
unix_type OS is supported.
Changes in version 1.19.1:
o BUGFIX: Updated NAMESPACE file to conform with R CMD check.
o BUGFIX: reactome2cmap function is available again.
o NEW: Added citation information.
Changes in version 1.17.3:
o BUGFIX: Simpified the mergeCMAPs function.
o BUGFIX: Added additional imports to NAMESPACE, as recommended by R
CMD check.
Changes in version 1.17.2:
o BUGFIX: Added import of the Matrix package to NAMESPACE file.
Changes in version 1.17.0:
o BUGFIX: Added camera's newly introduced inter.gene.cor parameter in
camera_score-methods.
Changes in version 1.11.3:
o BUGFIX: The wiki2cmap function now excludes empty files downloaded
from wikipathways from parsing.
o BUGFIX: The go2cmap function is now exported.
o BUGFIX: The reactom2cmap function is currently defunct, because the
reactome.db package is broken.
Changes in version 1.11.2:
o CHANGE: Fixed typo in mroast_score method.
Changes in version 1.11.1:
o BUGFIX: Fixed the romer_score method to accomodate the change in
argument order in limma's romer function.
Changes in version 1.11.0:
o CHANGE: Version bump for BioC update.
Changes in version 1.10.0:
o CHANGE: Version bump for BioC update.
Changes in version 1.9.2:
o BUGFIX: Updated geneIndex method to accept both symbols2indices and
id2indices functions from limma, depending on the limma version.
Changes in version 1.8.1:
o BUGFIX: Updated extraction of big.max objects while maintaining
row.names.
Changes in version 1.7.2:
o CHANGE: Helper functions KEGG2cmap, reactome2cmap, wiki2cmap and
go2cmap have two additional parameters, min.size and max.size,
restricting the output to gene sets containing members within the
specified range.
o CHANGE: Method camera_score now outputs correlations in column
'effect'.
o BUGFIX: Correct numbers of annotated genes are now returned for each
set.
Changes in version 1.7.1:
o CHANGE: Vignettes are now stored in vignettes directory.
Changes in version 1.5.4:
o NEW: The bigmemory and bigmemoryExtras packages are not optional,
enabling use of gCMAP on Windows
Changes in version 1.5.3:
o NEW: Updated titles of vignettes
Changes in version 1.5.2:
o BUGFIX: Updated eSet construction in mapNmerge function
Changes in version 1.5.1:
o BUGFIX: fixed incorrect varMetaData element definition in
.process_counts
Changes in version 1.3.5:
o NEW: DESeq package is now listed as 'Suggested' instead of 'Depends'
Changes in version 1.3.4:
o NEW: Removed lattice and reshape dependencies.
o NEW: Removed cmapQAPlot function.
o NEW: Added generate_gCMAP_NChannelSet's 'report.center' parameter.
Changes in version 1.3.3:
o NEW: Experimented with cmapQAPlot function (removed again in version
1.3.4).
Changes in version 1.3.2:
o NEW: mgsa_score method wrapping the model-based gene set analysis
approach available in the mgsa package.
Changes in version 1.3.1:
o NEW: KEGG2cmap, reactome2cmap, wiki2cmap and go2cmap to functions to
generate CMAPCollections from public annotation databases
o NEW: upIds and downIds methods for CMAPCollection objects.
Changes in version 1.3.0:
o NEW: fisher_score method now accepts NChannelSets as 'sets' and
thresholds a channel of choice on the fly.
o BUGFIX: induceCMAPCollection method was updated to fix a bug that
prevented processing of certain single-sample eSets.
o NEW: parameters 'center.z' and 'center.log_fc' for the
generate_gCMAP_NChannelSet function, centering each column of the
score matrix on the column mean, median or density peak.
(Internally, the NEW: 'center_eSet' function is called.)
o NEW: function 'center_eSet' to center columns of eSet channels on
either their kernel density peak, their mean or their median.
o NEW: function mergeCMAPs to combined two eSets that share class,
varLabels, annotation and assayDataElementNames.
o BUGFIX: Fixed missing gene names in featureScores method with
CMAPCollections queries containing single-gene sets.
o NEW: splitPerturbations function to split ExpressionSet (e.g.
downloaded from ArrayExpress) by annotations provided in the
phenoData slot.
o NEW: eset_instances function to generate lists eSets from larger
datasets by specifying an instance.matrix.
o NEW: setSizes methods for CMAPCollections returns a data.frame with
the number of members for each gene set stored in the Collection.
o NEW: fisher_score method now reports z-scores in the effect column
instead of log-odds-ratio. The latter are returned in the NEW: ,
separate LOR column.
o NEW: featureScores method now return list of matched identfiers when
dispatched on two CMAPCollection.
o NEW: Added 'density.only', 'level.only' and 'strip.only' parameters
to the CMAPResults plot method to selectively return only one plot
component.
o IMPROVED Reduced memory footprint of gsealm_jg_score and
induceCMAPCollection methods.
o CHANGED: By default, 'removeShift' option for gsealm_jg_score and
gsealm_score methods is now set to FALSE.
o BUGFIX: Corrected sign of effect size for fisher_score for perfect
overlap between set and query.
o IMPROVED: Improved plot method for CMAPResults objects, lattice
package is no longer required.
Changes in version 1.1.4:
o BUGFIX: The gealm_score method is not defined for queries with
missing values and will now return the corresponding error message.
o BUGFIX: GeneSetCollections containing only one set are processed
correctly by gsealm_score.
Changes in version 1.1.3:
o BUGFIX: Corrected sign of effect size for fisher_score for perfect
overlap between set and query.
Changes in version 1.1.2:
o BUGFIX: Fixed log-odds calculation in fisher_score: non-overlapping
sets now get a log odds ratio of 0
Changes in version 1.1.1:
o IMPROVED: Reduced memory footprint of induceCMAPCollection method
for bigmemory-backed eSet objects.
Changes in version 1.1.0:
o NEW: Version number was increased for the Bioconductor release.
Changes in version 0.99.6:
o IMPROVED: Updated mapIdentifiers method for SignedGeneSet class now
handles more different annotation types.
Changes in version 0.99.5:
o NEW: The BigMatrix package changed its name to bigmemoryExtras.
Currently, bigmemoryExtras only supports Mac and Unix platforms,
thus gCMAP does not support Windows, either.
Changes in version 0.99.1:
o NEW: First release of the gCMAP package to Bioconductor.