get_mirtarbase: Get validated targets for miRNAs using miRTarBase database

In kassambara/miRTarget: Find miRNA targets

Description

miRTarBase (http://mirtarbase.mbc.nctu.edu.tw/index.php) is an experimentally validated microRNA-target interactions (MTIs) database. MTIs are validated experimentally by reporter assay, western blot, microarray and next-generation sequencing experiments. The miRTarBase provides the most updated collection by comparing with other similar, previously developed databases.

• get_mirtarbase_vt(): Download validated targets for each miRNA using miRTarBase. Internet connexion is required.

Usage

get_mirtarbase_vt(miRNAs, species = "Homo sapiens", version = 6.1)

Arguments

miRNAs	a character vector containing miRNA names (e.g.: miRNAs = c("hsa-miR-16", "hsa-miR-34a))
species	of interest as available on miRTarbase (see http://mirtarbase.mbc.nctu.edu.tw/php/download.php). Allowed values are one of: 'Arabidopsis thaliana', 'Bombyx mori', 'Bos taurus', 'Caenorhabditis elegans', 'Drosophila melanogaster', 'Danio rerio', 'Epstein Barr virus', 'Gallus gallus', 'Human cytomegalovirus', 'Homo sapiens', 'Kaposi sarcoma-associated herpesvirus', 'Mus musculus', 'Ovis aries', 'Oryza sativa', 'Rattus norvegicus', 'Vesicular stomatitis Indiana virus', 'Xenopus laevis', 'Xenopus tropicalis'.
version	the current version of miRTarbase

Value

• get_mirtarbase_vt(): Downloads and returns an object of class .MirTarget which is a data frame containing validated targets for each miRNA. Internet connexion is required.

Author(s)

Alboukadel Kassambara [e-mail]

References

A. Kassambara. Statistical Tools for High-throughput Data Analysis. http://www.sthda.com

Examples

## Not run: 
# 3. Get validated targets for miRNA of interest
 vtget <- get_mirtarbase_vt(c("hsa-miR-16", "hsa-miR-155"))

 head(vtget)

## End(Not run)

kassambara/miRTarget documentation built on May 20, 2019, 7:40 a.m.