MirnahostgenesDb-class: miRNA host gene definitions
In jotsetung/mirhostgenes: mirhostgenes: putting miRNAs into genomic context

Description Usage Arguments Objects from the Class Slots Basic usage Author(s) See Also Examples

Basic functionality for miRNA host gene packages. Such database packages can be created using the makeMirhostgenesPackage function (see the corresponding help page for more information).

For methods and examples to retrieve host gene definitions and similar from the database, refer to the hostgenes man page.

## S4 method for signature 'MirhostDb'
dbconn(x)

## S4 method for signature 'MirhostDb'
listArrays(x, ...)

## S4 method for signature 'MirhostDb'
listColumns(x, table, skip.keys=TRUE, ...)

## S4 method for signature 'MirhostDb'
listTables(x, ...)

## S4 method for signature 'MirhostDb'
listDatabases(x, ...)

## S4 method for signature 'MirhostDb'
listGenebiotypes(x, ...)

## S4 method for signature 'MirhostDb'
listTxbiotypes(x, ...)

## S4 method for signature 'MirhostDb'
metadata(x)

## S4 method for signature 'MirhostDb'
mirbaseVersion(x)

MirhostDb(x)

## S4 method for signature 'MirhostDb'
organism(object)

## S4 method for signature 'MirhostDb'
version(object, what="ensembl", ...)

`...`	Additional arguments. For not used for any methods.
`object`	For `version` and `organism`: the `MirhostDb` instance for which the version of the miRBase or Ensembl database should be returned.
`skip.keys`	For `listColumns`: whether primary and foreign keys should be returned.
`table`	For `listColumns`: specify the database table name for which the columns should be listed.
`what`	For `version`: either `"ensembl"` or `"mirbase"` specifying the resource for which the version used to build the database should be returned.
`x`	For `MirhostDb` the file name of the SQLite database file with the host gene data (as created by the `makeHostgeneSQLiteFromTables` function). For all other methods the `MirhostDb` instance.

A connection to the respective annotation database is created upon loading of an annotation package created with the makeMirhostgenesPackage function. See examples below for basic usage.

con: Object of class "DBIConnection": the connection to the database.
tables: named list of database table columns with the names being the database table names. The order in which the tables are returned are the by their degree, i.e. the number of other tables they can be connected to (joined with).
have_pre_sequence: Logical specifying whether a database table with pre-miRNA sequences in available.
have_mirfam: Logical specifying whether a database table with miRNA family definitions is available.
have_array_features: Logical specifying whether a database table with microarray features (probe sets) is available.
have_premirna_confidence: Logical specifying whether pre-miRNA confidence information, as provided by the miRBase database, is available.
have_premirna_readcount: Logical specifying whether the read counts information for pre-miRNAs as provided by the miRBase database is available.
have_matmirna_confidence: Logical specifying whether mature miRNA confidence information, as provided by the miRBase database, is available.
have_matmirna_readcount: Logical specifying whether the read counts information for mature miRNAs as provided by the miRBase database is available.

(in alphabetical order)

dbconn: Returns the SQLiteConnection connection to the internal database.
listArrays: Returns a character vector with the names of the microarrays for which probe set to host transcript mappings are available.
listColumns: Returns a character vector of all columns stored in a database, or in a single database table if table was specified.
listDatabases: Returns a character vector of all databases from which gene/transcript models for host gene predictions were retrieved. In most instances the databases "core" (Ensembl core), "otherfeatures" (Ensembl otherfeatures containing CCDs and RefSeq genes) and "vega" (Ensembl Vega database with curated genes) are queried.
listGenebiotypes: Returns a character vector of all available gene biotypes from the database. These values can be used in a GenebiotypeFilter to filter results queried from the database.
listTables: Returns a named list of database table columns (names of the list being the database table names).
listTxbiotypes: Returns all available transcript biotypes from the database. These values can be used in a TxbiotypeFilter to filter results queried from the database.
metadata: Retrieves the metadata of the database. Returns a data.frame with the key-value pairs.
mirbaseVersion: Returns the version of the miRBase database the MirhostDb database bases on as a character string.
MirhostDb: The constructor function. Returns a MirhostDb instance.
organism: Returns the organism (e.g. "Homo sapiens").
show: Displays some informations from the database.
version: Returns the version of the resource (either Ensembl or miRBase) that was used to build the database.

Johannes Rainer

hostgenes, premirnas, makeMirhostgenesPackage, PositionFilter

library(MirhostDb.Hsapiens.v75.v20)
## make a shortcut...
mhg <- MirhostDb.Hsapiens.v75.v20

## show some information of the database
mhg


## the version of the Ensembl database
ensemblVersion(mhg)

## the version of the mirbase database
mirbaseVersion(mhg)

## list all tables along with their columns
listTables(mhg)

## list all columns stored in the database for database table host_tx
listColumns(mhg, table="host_tx")

## list all databases on which gene/transcript models host genes were
## defined
listDatabases(mhg)

## for what organism is this package
organism(mhg)

## list all available gene biotypes
listGenebiotypes(mhg)

## list all available transcript biotypes
listTxbiotypes(mhg)

## list all microarrays for which probe sets have been indentified
## targeting the host genes/transcripts
listArrays(mhg)

## get an overview of the full metadata
metadata(mhg)

## get some information about the genome
genome(mhg)

## or the chromosomes on which the miRNA precursors (pre-miRNAs)
## where defined
seqinfo(mhg)