getAvailableSpecies: Retrieve various content from the miRTarBase.

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

Description

These functions return all various informations from the miRTarBase. getAvailableSpecies: Returns the species of miRNAs or genes from the database.

getSupportTypes: Returns a unique list of support types (and evidences) for a miRNA target interaction.

getAvailableExperiments: Returns a unique list of experiments that have been performed.

getPmids: Returns the PubMed identifiers of all publications in the database.

Usage

getAvailableSpecies( x="target_gene" )
getSupportTypes()
getAvailableExperiments( split="//" )
getPmids()

Arguments

x	For which the species should be returned. Either “target_gene” or “mirna”.
split	By default experiments providing evidence for a miRNA target gene interaction in a publication are separated by “//” in the miRTarBase. The function getAvailableExperiments thus splits the entry in the database using the provided character to return a unique list of experiments.

Value

A character vector of species names, support types, experiments or a numerical vector of PubMed identifiers.

Author(s)

Johannes Rainer

Examples

## get available species for miRNAs
getAvailableSpecies( "mirna" )

## get available species for target genes
getAvailableSpecies( "target_gene" )

## get all support types from the database
getSupportTypes()

## get a list of experiments
Exps <- getAvailableExperiments()

## get a list of PubMed IDs
getPmids()

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