v1.1.5 Bugfixes: - Fixed minor bug in database setup that caused instability with cuffdiff --no-diff argument. - Fixed bug in csDendro method for CuffData objects. v1.1.4 New Features: - Added MAplot() method to CuffData objects. Bugfixes: - Finished abrupt migration to reshape2. As a result fixed a bug in which 'cast' was still required for several functions and could not be found. Now appropriately using 'dcast' or 'acast'. - Fixed minor bug in CuffFeature::fpkmMatrix v1.1.3 New Features: - getSig() has been split into two functions: getSig() now returns a vector of ids (no longer a list of vectors), and getSigTable() returns a 'testTable' of binary values indicating whether or not a gene was significant in a particular comparison. - Added ability in getSig() to limit retrieval of significant genes to two provided conditions (arguments x & y). (reduces time for function call if you have a specific comparison in mind a priori) * When you specify x & y with getSig(), q-values are recalculated from just those selected tests to reduce impact of multiple testing correction. * If you do not specificy x & y getSig() will return a vector of tracking_ids for all comparisons (with appropriate MTC). - You can now specify an 'alpha' for getSig() and getSigTable() [ 0.05 by default to match cuffdiff default ] by which to filter the resulting significance calls. - Added csSpecificity() method: This method returns a feature-X-condition matrix (same shape as fpkmMatrix) that provides a 'condition-specificity' score * defined as 1-(JSdist(p,q)) where p is is the density of expression (probability vector of log(FPKM+1)) of a given gene across all conditions, and q is the unit vector for that condition (ie. perfect expression in that particular condition) * specificity = 1.0 if the feature is expressed exclusively in that condition - Created csDendro() method: This method returns a object of class 'dendrogram' (and plots using grid) of JS distances between conditions for all genes in a CuffData, CuffGeneSet, or CuffFeatureSet object. * Useful for identifying relationships between conditions for subsets of features - New visual cues in several plot types that indicates the quantification status ('quant_stat' field) of a particular gene:condition. This information is useful to indicate whether or not to trust the expression values for a given gene under a specific condition, and may provide insight into outlier expression values. * This feature can be disabled by setting showStatus=F. - csDensity() is now available for CuffFeatureSet and CuffGeneSet objects Bugfixes: - Fixed bug in getGenes that may have resulted in long query lag for retrieving promoter diffData. As a result all calls to getGenes should be significanly faster. - CuffData fpkm argument 'features' now returns appropriate data.frame (includes previously un-reported data fields). - Replaced all instances of 'ln_fold_change' with the actual 'log2_fold_change'. Values were previously log2 fold change but database headers were not updated to reflect this. - Fixed bug that could cause readCufflinks() to die with error when using reshape2::melt instead of reshape::melt. Notes: - ***The structure of the underlying database has changed in this version. As a consequence, you must rebuild you cuffData.db file to use new version. readCufflinks(rebuild=T)*** - Updated vignette - A 'fullnames' logical argument was added to fpkmMatrix. If True, rownames for fpkmMatrix will be a concatenation of gene_short_name and tracking_id. This has the added benefit of making row labels in csHeatmap easier to read, as well as preserving uniqueness. - Slight speed improvements to JSdist (noticeable when using csCluster on large feature sets). - 'testTable' argument to getSig() has been dropped in lieu of new getSigTable() method. v1.1.1 Bugfixes: - fixed issue in which there was no graceful error handling of missing CDS or TSS data in cuffdiff output. - Fixed issue in which distribution test data (promoters, splicing, relCDS) were not appropriately added to objects on creation. - Fixed bug that would sometimes cause csBoxplot() to throw an error when log-transforming fpkm data. Also added pseudocount argument. - Fixed bug that would cause diffData() to return a filtered subset of results by default. - Adjusted indexing of tables to improve performance on large datasets. - Fixed bug that caused diffData method to not be registered with CuffFeature and CuffGene objects. - Fixed bug that sometimes caused over-plotting of axis labels in csBarplots. New Features: - added getSig method to CuffSet class for rapid retrieval of significant features from all pairwise tests (as a list of IDs). By default the level is 'genes' but any feature level can be queried. - csCluster now uses Jensen-Shannon distance by default (as opposed to Euclidean) - Added 'xlimits' argument to csVolcano to constrain plot dimensions. - Enforced requirement in csVolcano for x and y arguments (as sample names). Notes: - Changed dependency 'reshape' to 'reshape2' - Changed the default orientation of expressionBarplot() for CuffFeatureSet objects. - Changed output of csCluster to a list format that includes clustering information. As a result, I created the function csClusterPlot to replace the previous default drawing behavior of csCluster. This allows for stable cluster analysis. - For consistency, the 'testId' slot for CuffDist objects was renamed to 'idField'. This brings the CuffDist class in line with the CuffData class. - CuffGene and CuffGeneSet now include slots for promoter, splicing, and relCDS distribution test results. v1.0.0 - Official public release. No changes from v0.99.5 v0.99.5 - Significant speed improvements to readCufflinks() for large cuffdiff datasets. - Tables written first then indexed. - Added slot accessor methods to avoid using slots directly. v0.99.4 - Second beta release and submission to Bioconductor v0.1.3 Release 2011-08-18: - First Beta release of cummeRbund and submission to Bioconductor for review and hosting.