NEWS

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ribiosAnnotation 3.2-0 (2016-12-21)

• Add mRNArefseqByTaxID to get all refseq IDs given a Taxonomy ID

ribiosAnnotation 3.1-8 (2015-06-30)

• export annotateAnyIDs to annotate any types of feature identifiers supported by GTI

ribiosAnnotation 3.1-7 (2015-01-15)

• hasOracle uses now the 'requireNamespace' function to test whether ROracle can be loaded or not. This is more robust than testing the binary of sqlplus.
• No Depends packages any more. Both ribiosUtils and DBI are imported from.

ribiosAnnotation 3.1-6 (2014-10-10)

• Java heap size is set to 4g before library loading if RJDBC has to be used. This will eliminate memory error messages due to insufficient heap size.

ribiosAnnotation 3.1-5 (2014-07-08)

• Add annotatemRNAs to translate mRNA accession numbers to GeneIDs.
• Todo: there are redundant codes in annotateProbesets.R, with regard to multiple annotation methods. They should be cleaned-up.

ribiosAnnotation 3.1-4 (2014-04-02)

• ribiosCon tests whether RJDBC exists before it tries the JDBC option
• Add importFrom DBI and ribiosUtils
• Makefile: the R-devel default location is changed to point to the version that runs both on montale and bedastats

ribiosAnnotation 3.1-3 (2013-11-14)

• fillOneColTmpTbl:empty values are handled correctly.

ribiosAnnotation 3.1-2 (2013-10-16)

• Debug: in .onAttach, the ROracle namespace is not attached when it has been attached before. It fixes a bug that ribiosAnnotation refuses to be loaded when the ROracle package has been loaded before

ribiosAnnotation 3.1-1 (2013-10-11)

• add annotateEnsembl to annotate ENSEMBL identifiers

ribiosAnnotation 3.1-0 (2013-07-08)

• annotateHumanOrthologs: if multiple human orthologs were found and when multiple orthologues are not required, the one with the smallest GeneID (as integer) will be reported as the orthologue.
• Remove illuminaSnp function: the table has been deleted in the database.

ribiosAnnotation 3.0-6 (2013-01-22)

• annotateHumanOrthologs: the output data.frame puts shorter GeneSymbols in front of longer ones in case one ID is mapped to several items; useful for reducing mismatch rates in annotating orthologues.

ribiosAnnotation 3.0-5 (2012-10-24)

• annotateAnyID passes on the 'chip' option to annotateProbesets

ribiosAnnotation 3.0-4 (2012-10-22)

• Add scriptChiptypes and annotateAnyID to simply annotations in Rscripts

ribiosAnnotation 3.0-3 (2012-10-03)

• Add ribios_orthologizer.Rscript to convert identifiers (GeneID, GeneSymbol or probesets) from other organisms to human

ribiosAnnotation 3.0-2 (2012-08-27)

• Bug fix: annotateHumanOrthologs returns a data.frame of five columns (previous four), adding a column OrigTaxID holding the TaxID of querying GeneIDs. The column GeneID is fixed as 9606, the TaxID of human.
• Add internal function annotateHumanOrthologsNoOrigTax to remove OrigTaxID column, used by internal functions to make orthologue mapping.

ribiosAnnotation 3.0-1 (2012-08-22)

• Bug fix: querydbTmpTbl works well with NA values. Remaining bug: if no valid identifiers are given, the function stops and reports error.

ribiosAnnotation 3.0-0 (2012-07-26)

• Substantial updates of querydb, querydbSelectIn and querydbTmpTbl to support annotating anywhere.
• From this version, ribiosAnnotation does not strictly depend on the availability of Oracle client library. It can run anywhere with JDBC accessing Oracle data.

ribiosAnnotation 2.0-1 (2012-07-16)

• annotateProbesets: If the option 'chip' is not missing, 'gtiChipAnnotation' takes over the orthologue mapping task, which was missing in previous versions.

ribiosAnnotation 2.0-0 (2012-06-20)

• Substantial upgrades of following functions: annotateProbesets, annotateGeneIDs and annotateGeneSymbols
• For probesets mapping, three functions are available for different scenarios: gtiChipAnnotation, annotateAnyProbeset, and guessChiptype
• Consistently map probesets, GeneIDs and GeneSymbols to Orthologues
• Add annotateHumanOrthologs to map any Entrez GeneID to human orthologues
• Add querydbTmpTbl to fill temporary table with user inputs and perform JOIN actions.
• Speed-up several functions
• Next major release will make the package work both with ROracle or RJDBC.

ribiosAnnotation 1.2-0 (2012-06-12)

• annotateProbesets, annotateGeneIDs and annotateGeneSymbols are substantially improved: they use now GTI tables, and are able to map orthologues.
• querydbSelectIn has been exported, and documented.
• TODO: currently the password are saved in clear text. This should be encoded.

ribiosAnnotation 1.1-0 (2012-03-22)

• querydb and querydbSelectIn have been refactored. They now accept db, user and password as inputs to provide more flexibility for programmer. The change is however transparent to end users, they should not have to remember which database to connect to and what are authentication details.
• TODO: currently the password are saved in clear text. This should be encoded.

ribiosAnnotation 1.0-18 (2012-03-15)

• Add humanOrthologs, humanUniqOrtholog, nonhumanOrthologs and nonhumanUniqOrtholog to get ortholog information from GTI

ribiosAnnotation 1.0-17 (2012-02-21)

• Add newconRED(), enabling query the bia database with permissions of the user 'red' (for example CNS NGS data)
• Modify querydb in order to allow querying database with red

ribiosAnnotation 1.0-16 (2012-02-13)

• the ORA object assignment is done after exporting ORACLE.BASE and ORACLE.LIB, to adapt to the newest version (1.1-1) of ROracle package
• the gtiChipAnnotation function does not break when no probeset was annotated (due to logical(0) before)

ribiosAnnotation 1.0-15 (2012-02-10)

• gtiChiptypes uses genome.CHIP_ARRAY_TYPES@bin table to report GTI-supported chip types. Comparing previous versions, the default behavior is not changing. By settign 'include.desc=TRUE', more details are returned, includeing Technology and Species.
• gtiChipAnnotation uses genome.chip_probeset_gene and genome.GTI_GENES internally, in order to be 100% synchronized with GTI. The resulting data.frame keeps consistency, although the isSingleGeneID column is always set to TRUE since only uniquely mapped probesets are stored. Provisionally this column shall be removed in the future version.
• We export the hapmapSnp and illuminaSnp functions thanks to Isabelle's help. They are able to query SNP annotation and genomic contexts with user input.

ribiosAnnotation 1.0-14 (2012-02-07)

• Add isGtiChiptype to check user input with GTI-supported chiptypes
• Change the default order of 'db' in the querydb function to c("bia", "bin")
• gtiChipAnnotation has been substantially refactored: that for queries <1000 items, the filtering is done by the IN syntax of SQL instead by R. Doing so saves much overhead of transfering large tables between SQL and R. A benchmark with random sampled GeneIDs (see codes in the test directory) showed a 5-10x better performance measured by the running time.
• gtiChipAnnotation documentation has been correspondingly updated
• ORACLE.IN.NMAX constant variable is exported: the maximum length of the vector in the IN query syntax
• Add mappedProbesets to get all probesets that map to given Entrez GeneIDs.
• We have solved the mysterious issue of example codes in the ribiosAnnotation package:by wrapping example codes with options(error=utils:recover) and options(error=NULL), the examples can be executed now in the check process without issuing error. Although we do not really know why this is the case, this information should be shared with all developers who have had similar problems.

ribiosAnnotation 1.0-13 (2012-02-03)

• Add querydb to make generic db queries
• Add chrLen to query chromosome lengths in supported organisms

ribiosAnnotation 1.0-12 (2012-02-02)

• gtiTaxAnnotation returns MappedChr, CoordLeft, CoordRight and RevComp for chromosome-mapping information, by outer joining the genome.gti_gene_map_a@genome table
• Internal: connection to the bia server ia authenticated by bi.
• gtiChipAnnotation (and downstream annotateProbesets) uses 'bi.EG_GENE_INFO.OFFICIAL_SYMBOL' for GeneSymbol instead of 'bi.AFFYCHIP_XREF_LL.GN'

ribiosAnnotation 1.0-11 (2012-02-01)

• Add gtiTaxAnnotation.Rd to get annotations belonging to the given TaxonID.
• Change newcon to newconBIA, add newconBIN to prepare for connection to the BIN server

ribiosAnnotation 1.0-10 (2012-01-25)

• annotateIDs sets the queried IDs in its column, which affects annotateProbesets, annotateGeneIDs and annotateGeneSymbols

ribiosAnnotation 1.0-9 (2012-01-24)

• Add annotateGeneIDs and annotateGeneSymbols to annotate GeneIDs/GeneSymbols in a similar fashion as that for probesets
• annotateProbeIDs have been added as a synonym to annotateProbesets
• Internally the core logic of annotateProbesets is refactored into \code{annotateIDs} to be shared by \code{annotateGeneIDs} and \code{annotateGeneSymbols}.
• Add a Rscript to do annotation from command line: inst/Rscript/ribios_annotate.R
• Add test bash file and test text files for ribios_annotate.Rscript

ribiosAnnotation 1.0-8 (2012-01-06)

• bioc2gti and gti2bioc support missing argument. If 'chipname' is left missing, the functions will print GTI/Bioc names of chip types supported by both GTI and Bioc.

ribiosAnnotation 1.0-7 (2011-12-21)

• Add join of bi.EG_GENE_INFO to gtiChipAnnotation, in order to get GeneNames

ribiosAnnotation 1.0-6 (2011-12-20)

• Following suggestions of Laura, the race prefix is changed into gti
• Thanks for Stan's feedback: ORACLE_BASE and ORACLE_HOME environment variables are set in the .onLoad function
• ORACLE_BASE is set when there is no environment variable, or the path pointed to by the variable does not contain the "client" subfolder.
• ORACLE_HOME is set when there is no environment variable, or the path pointed to by the variable does not contain the "bin" subfolder.
• To test the ribiosAnnotation in a free environment, use "exec env -i bash --norc".

ribiosAnnotation 1.0-4 (2011-12-16)

• Current functions have been renamed to better reflect their functions
• raceChiptypes (aka raceChipnames) returns a list of supported chip types (in the form of character vector)
• raceChipAnnotation provides all annotation information for a certain chip
• annotateProbesets provides annotation information for queried probesets.
• The version numbering system is now consistent with the R convention (x.y-z)

ribiosAnnotation 1.0.3 (2011-12-15)

• Only BIOS-specific functions have been kept in the new ribiosAnnotation package, other functions relying on Bioc annotation mechanisms have been moved to the ciocAnnotation package, which shall not be part of the ribios suite).
• Functions are renamed in a consistent way, representing their functionality. The old names are deprecated.