Collect information about the package annotation DB
SomaScan_dbconn.RdSome convenience functions for getting a connection object to (or collecting information about) the package annotation DB.
Usage
SomaScan_dbconn()
SomaScan_dbfile()
SomaScan_dbschema(file="", show.indices=FALSE)
SomaScan_dbInfo()Arguments
- file
A connection, or a character string naming the file to print to (see the
fileargument of thecatfunction for the details).- show.indices
The CREATE INDEX statements are not shown by default. Use
show.indices=TRUEto get them.
Details
SomaScan_dbconn returns a connection object to the
package annotation DB. IMPORTANT: Don't call
dbDisconnect on the connection object
returned by SomaScan_dbconn or you will break all the
AnnDbObj objects defined
in this package!
SomaScan_dbfile returns the path (character string) to the
package annotation DB (this is an SQLite file).
SomaScan_dbschema prints the schema definition of the
package annotation DB.
SomaScan_dbInfo prints other information about the package
annotation DB.
Value
SomaScan_dbconn: a DBIConnection object representing an
open connection to the package annotation DB.
SomaScan_dbfile: a character string with the path to the
package annotation DB.
SomaScan_dbschema: none (invisible NULL).
SomaScan_dbInfo: none (invisible NULL).
Examples
library(DBI)
## Count the number of rows in the "probes" table:
dbGetQuery(SomaScan_dbconn(), "SELECT COUNT(*) FROM probes")
#> COUNT(*)
#> 1 10870
SomaScan_dbschema()
#> CREATE TABLE metadata (name VARCHAR(80) PRIMARY KEY, value VARCHAR(255) );
#> CREATE TABLE map_metadata (
#> map_name VARCHAR(80) NOT NULL,
#> source_name VARCHAR(80) NOT NULL,
#> source_url VARCHAR(255) NOT NULL,
#> source_date VARCHAR(20) NOT NULL
#> );
#> CREATE TABLE map_counts (
#> map_name VARCHAR(80) PRIMARY KEY,
#> count INTEGER NOT NULL
#> );
#> CREATE TABLE sqlite_stat1(tbl,idx,stat);
#> CREATE TABLE accessions (probe_id VARCHAR(80),accession VARCHAR(20));
#> CREATE TABLE probes (probe_id VARCHAR(80), gene_id VARCHAR(10) NULL, is_multiple SMALLINT NOT NULL);
#>
SomaScan_dbInfo()
#> name
#> 1 DBSCHEMAVERSION
#> 2 Db type
#> 3 Supporting package
#> 4 DBSCHEMA
#> 5 ORGANISM
#> 6 SPECIES
#> 7 MANUFACTURER
#> 8 CHIPNAME
#> 9 MANUFACTURERURL
#> 10 EGSOURCEDATE
#> 11 EGSOURCENAME
#> 12 EGSOURCEURL
#> 13 CENTRALID
#> 14 TAXID
#> 15 GOSOURCENAME
#> 16 GOSOURCEURL
#> 17 GOSOURCEDATE
#> 18 GOEGSOURCEDATE
#> 19 GOEGSOURCENAME
#> 20 GOEGSOURCEURL
#> 21 KEGGSOURCENAME
#> 22 KEGGSOURCEURL
#> 23 KEGGSOURCEDATE
#> 24 GPSOURCENAME
#> 25 GPSOURCEURL
#> 26 GPSOURCEDATE
#> 27 ENSOURCEDATE
#> 28 ENSOURCENAME
#> 29 ENSOURCEURL
#> 30 UPSOURCENAME
#> 31 UPSOURCEURL
#> 32 UPSOURCEDATE
#> value
#> 1 2.1
#> 2 ChipDb
#> 3 SomaScan.db
#> 4 HUMANCHIP_DB
#> 5 Homo sapiens
#> 6 Human
#> 7 SomaLogic
#> 8 SomaScan
#> 9 https://somalogic.com/somascan-platform/
#> 10 2023-Sep11
#> 11 Entrez Gene
#> 12 ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
#> 13 ENTREZID
#> 14 9606
#> 15 Gene Ontology
#> 16 http://current.geneontology.org/ontology/go-basic.obo
#> 17 2023-07-27
#> 18 2023-Sep11
#> 19 Entrez Gene
#> 20 ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
#> 21 KEGG GENOME
#> 22 ftp://ftp.genome.jp/pub/kegg/genomes
#> 23 2011-Mar15
#> 24 UCSC Genome Bioinformatics (Homo sapiens)
#> 25
#> 26 2023-Aug20
#> 27 2023-May10
#> 28 Ensembl
#> 29 ftp://ftp.ensembl.org/pub/current_fasta
#> 30 Uniprot
#> 31 http://www.UniProt.org/
#> 32 Mon Sep 18 16:12:39 2023