getMirbaseForMature: Retrieves various information for a mature miRNA ID from the...

In jotsetung/mirtarbase-db: miRTarBase miRNA-target interaction database

Description

This functions returns a data.frame with various informations for a given mature miRNA ID from the mirbase database (provided by the mirbase.db Bioconductor package).

getMirbaseForMature: search for a single miRNA.

mgetMirbaseForMature: search for multiple miRNAs.

Usage

getMirbaseForMature( x, operator="=", tables=c( "mirna" ) )
mgetMirbaseForMature( x, operator="=", tables=c( "mirna" ), ifnotfound=NA )

Arguments

x	The mature miRNA ID(s).
operator	The operator to search for the miRNA IDs. One of “=”, “!=”, “like” and “not like”.
tables	Character vector of the tables from which information should be returned. Currently “mirna” (informations about the pre-miRNA), “mirna\_prefam” (miRNA family information), “mirna\_cluster” (miRNA cluster) and “mirna_chromosome_build” (chromosomal alignment of the pre-miRNA) are supported.
ifnotfound	Will be returned if a miRNA is not found.

Details

The function returns the contents of the mirbase database tables “mirna\_mature” and “mirna”.

Value

A data.frame or a list of data.frames (in the case of mgetMirbaseForMature).

Author(s)

Johannes Rainer

Examples

Res <- getMirbaseForMature( x="hsa-miR-221-3p" )
colnames( Res )

Res <- mgetMirbaseForMature( c( "hsa-miR-221-3p", "hsa-miR-221-5p" ) )
class( Res )
length( Res )

## join to a data.frame
Res <- do.call( "rbind", Res )

## the call below is identical to getMirbaseFamForMature
Res <- getMirbaseForMature( "hsa-miR-221-3p", tables=c( "mirna", "mirna_prefam" ) )

jotsetung/mirtarbase-db documentation built on May 19, 2019, 9:42 p.m.