Provides concrete implementation of GeneIDMap builder that uses annotations shipped with specified microarray; those annotations shall contain mapping between the individual probe(set)s and gene symbols. The currently implemented builder is tailored for processing of Affymetrix annotations. See Affymetrix annotations for more details. The mapping is based solely on the annotations, i.e. it does not check for obsolete or synonymous gene symbols in HGNC data. See HGNC_GPL for the builder that provides this functionality.
Bases: kdvs.fw.Map.GeneIDMap
GeneIDMap builder that uses Affymetrix annotations available at Gene Expression Omnibus. Annotations must already be loaded “as–is” into KDVS DB and wrapped into DSV instance. The mapping table follows EM2ANNOTATION_TMPL template.
Construct the mapping using resources already present in KDVS DB (via DBManager) and wrapped in DSV instances. The mapping is built as database table and wrapped into DBTable instance; it is stored in public attribute dbt of this instance. After the build is finished, the public attribute built is set to True. This builder requires Affymetrix annotations data already loaded in KDVS DB and wrapped in DSV instance.
Parameters : | anno_dsv : DSV
hgnc_dsv : DSV
map_db_key : string
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Raises : | Error :
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Provides concrete implementation of GeneIDMap builder that uses annotations shipped with specified microarray; those annotations shall contain mapping between the individual probe(set)s and gene symbols. The currently implemented builder is tailored for processing of Affymetrix annotations. See Affymetrix annotations for more details. The mapping is based both on the annotations and HGNC data, i.e. it tries to resolve obsolete or synonymous gene symbols into more usable ones.
Bases: kdvs.fw.Map.GeneIDMap
GeneIDMap builder that uses Affymetrix annotations available at Gene Expression Omnibus. Annotations must already be loaded “as–is” into KDVS DB and wrapped into DSV instance. HGNC data must be loaded and wrapped in DSV as well. The mapping table follows EM2ANNOTATION_TMPL template.
Construct the mapping using resources already present in KDVS DB (via DBManager) and wrapped in DSV instances. The mapping is built as database table and wrapped into DBTable instance; it is stored in public attribute dbt of this instance. After the build is finished, the public attribute built is set to True. This builder requires both Affymetrix annotations data and HGNC data already loaded in KDVS DB and wrapped in DSV instances. Refer to the comments for resolvancy protocol used.
Parameters : | anno_dsv : DSV
hgnc_dsv : DSV
map_db_key : string
|
---|---|
Raises : | Error :
Error :
|