MirnaDb-class {miRNAtap}R Documentation

Database class

Description

object of MirnaDb class holds the sqlite database connection, and extends AnnotationDb class from AnnotationDbi package. columns, keys, keytypes and select methods allow access to database tables and retrieval of miRNA target information.

select is the most important method, allows querying the database for predictions from a specific source and species for a given miRNA

Usage

columns(x)
keytypes(x)
keys(x, keytype, ...)
select(x, keys, columns, keytype, ...)

## S4 method for signature 'MirnaDb'
columns(x)

## S4 method for signature 'MirnaDb'
keytypes(x)

## S4 method for signature 'MirnaDb'
keys(x, keytype, ...)

## S4 method for signature 'MirnaDb'
select(x, keys, columns, keytype, ...)

Arguments

x

the MirnaDb object

keytype

the keytype that matches the keys used; the table in which the search should be performed.

...

any optional arguments

keys

the key to select records for from the database - miRNA name; all possible keys (miRNAs) are returned by using the keys method.

columns

in this case same as keytype, the table in which the search should be performed, this value specifies the source of predictions as well as species; as with keys, all possible columns are returned by using the columns method.

Value

string vectors, for select a data.frame with target genes and scores

Author(s)

Maciej Pajak m.pajak@sms.ed.ac.uk

Examples

#first load the annotations
require(miRNAtap.db)
#see all available tables
keytypes(miRNAtap.db)
[Package miRNAtap version 1.21.0 Index]