new.persistence.connection: Create a new persistence connection object
In jweile/maveclin: Clinical predictions for MaveDB

Description Usage Arguments Details Value Examples

Constructor for creating a new object of type persistence.connection. Each operation uses a mutex lock to secure the database.

1	new.persistence.connection(dbfile)

dbfile

the SQLite database file

Provides the following methods: \begindescription \itemisKnown(urn) checks whether a URN is known to the database \itemisLocked() checks whether the database is currently locked \itemgetDate(urn) retrives the lastModified date for the scoreset with the given URN \itemgetStatus(urn) retrieves the status of the scoreset with the given URN \itemsetStatus(urn) sets the status of the scoreset with the given URN to the given status. Permissible values are "new","pending","processing","calibrated",and "error". \itemgetParameters(urn) retrieves the calibration parameters for the scoreset with the given URN \itemsetParameters(urn,symbol,ensemblGeneID,mafCutoff,flip,homozygous) changes the parameters for the dataset with the given URN to the given values. \itemgetScoreset(urn) retrieves scoreset entry with the given URN \itemnewScoreset(urn,symbols,ensembl) adds a new scoreset with the given URN to the database and initializes its gene symbols and ensembl gene names to the given values. \itemgetGoldStandard(urn) retrives the set of gold standard variants for the given urn \itemgetVariants(urn) retrives all variants for the given URN \itemhasVariant(acc) checks whether the variant with the given accession exists \itemgetVariantDetail(acc) retrives all adata on the given variant \itemcalibrateScores(caliScores) applies the given calibrated scores to the variants in the database caliScores should be a data.frame with at the columns: accession, flippedScore, clinsig, maf, hom, set, llr, llrCIleft and llrCIright \itemsearchScoresets(query) retrives a table of scoresets for which any field matches the query \itemsearchVariants(query) retrieves a table of variants for which the hgvs string matches the query \itemgetPending() retrieves a list of URNs of scoresets that are currently in the 'pending' state. \enddescription

a new persistence.connection object

dbfile <- "maveclin.db"
persist <- new.persistence.connection(dbfile)
persist$isKnown("urn:mavedb:00000001-c-2")
persist$getStatus("urn:mavedb:00000001-c-2")
persist$setStatus("urn:mavedb:00000001-c-2","new")
persist$close()