Function reference • SomaScan.db

Query the Database

Methods for retrieving annotations from the SQLite database.

keys(<SomaDb>): The keys method for SomaDb objects

keytypes(<SomaDb>): The keytypes method for SomaDb objects

reexports columns: The columns method for SomaDb objects

select(<SomaDb>): The select method for SomaDb objects

mapIds(<SomaDb>): The mapIds method for SomaDb objects

SomaDb-class .SomaDb: The SomaDb S4 class

Data Objects

Objects provided with SomaScan.db

SomaScan.db SomaScan: Bioconductor annotation data package for SomaScan

DataObjects somascan_menu probe_list somascan_analytes: SomaScan Menu Character Vectors

Mapping Objects

Objects containing mappings between database keys (i.e. identifiers).

SomaScanALIAS2PROBE: Map between Common Gene Symbol Identifiers and SomaScan SeqIds

SomaScanENSEMBL SomaScanENSEMBL2PROBE: Map Ensembl gene accession numbers with Entrez Gene identifiers

SomaScanENTREZID SomaScanLOCUSID: Map between SomaScan SeqIds and Entrez gene identifiers

SomaScanENZYME SomaScanENZYME2PROBE: Map between SomaScan SeqIds and Enzyme Commission (EC) numbers

SomaScanGENENAME: Map between SomaScan SeqIds and gene names

SomaScanGO SomaScanGO2PROBE SomaScanGO2ALLPROBES: Map between SomaScan SeqIds and Gene Ontology (GO) identifiers

SomaScanMAP: Map between SomaScan SeqIds and cytogenetic maps/bands

SomaScanOMIM: Map between SomaScan SeqIds and Mendelian Inheritance in Man (MIM) identifiers

SomaScanORGANISM SomaScanORGPKG: The Organism information for SomaScan

SomaScanPATH SomaScanPATH2PROBE: Mappings between probe identifiers and KEGG pathway identifiers

SomaScanPMID SomaScanPMID2PROBE: Maps between SomaScan SeqIds and PubMed identifiers

SomaScanREFSEQ: Map between SomaScan SeqIds and RefSeq identifiers

SomaScanSYMBOL: Map between SomaScan SeqIds and Gene Symbols

SomaScanTARGETFULLNAME: Map between SomaScan SeqIds and the full name of the protein target

SomaScanUNIPROT SomaScanUNIPROT2PROBE: Map between Uniprot accession numbers and SomaScan SeqIds

Helpers

Miscellaneous functions for retrieving data or modifying query results.

addTargetFullName(): Add Target Full Name information to data frame

Accessor Functions

Convenience functions for accessing the database.

SomaScan_dbconn() SomaScan_dbfile() SomaScan_dbschema() SomaScan_dbInfo(): Collect information about the package annotation DB