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Bioconductor Changlog.
Thu, 26 Jun 2008
AnnotationDbi
fixed typo in the SQLForge vignette (collumn == column)
[/AnnotationDbi] permanent link
HilbertCurveDisplay
initial check-in of HilbertCurveDiaplay, at version 0.1.2
(earlier changes in Huber group SVN)
[/HilbertCurveDisplay] permanent link
flowCore
updates
RpsiXML
Version bumping: 0.0.3. This version added support of MatrixDB, at the same time the parsing routine is able to handle the situation where (1) one 'entrySet' has more than one 'entry' items (2) no 'interactorList' or 'interactorRef' is provided. In-line parsing of interactors are used in the second case. One open question is the problem of source ID redundancy in matrixDB, more than one source ID corresponds to one UniProt ID. Will be solved in later versions. This check-in passed R-2.8.0-devel and R-2.7.1 passing without moaning. by David
Function extension: supporting the adding of MatrixDB
Function extension: in case interactorList is not provided by the source file, now the parser will parse the in-line interactor information.
DEBUG: show method for psimi25InteractionEntry debugged for the problem of total interactor number not displayed
Function extension: support for MatrixDB added
Function extension in parsePsimi25Interactions: in case of duplicated interactors or interactions only the unique ones are returned
DEBUG: in case of only one element in entrySet, the first is returned. Checking passed
DEBUG: length(entrySet) > 1 but not >0
Function extension: parsePsimi25Interaction function now supports more than one 'entry' items in one 'entrySet' node
New functions: replace methods for interactors, , taxId, organismName and releaseDate added (all for psimi25InteractionEntry objects)
New functions: replace methods for interactors, , taxId, organismName and releaseDate added (all for psimi25InteractionEntry objects)
Biostrings
Refactored pairwiseAlignment to make it easier to obtain mismatch information. This involved added an additional slot to PairwiseAlignment objects and created mismatch methods for AlignedXStringSet and PairwiseAlignment objects.
Also renamed indels to indel.
lumi
Add verbose parameter to the functions
arrayQualityMetrics
add a function to convert RGList into an NChannelSet to prepare the data before using aQM
[/arrayQualityMetrics] permanent link