hoardeR (version 0.9.2)

targetScan: Retrieving miRNA target information from targetscan.org

Description

This function requests from the webpage targetscan.org the stored information for mirnas.

Usage

targetScan(mirna=NULL, species=NULL, release="7.1", maxOut=NULL)

Arguments

mirna

The name of the mirna (String).

species

The species identifier, see details (String).

release

The release version of targetscan.org.

maxOut

The amount of target genes, default (NULL) is all.

Value

A data.frame with the following columns

Ortholog

The ortholog name of the target gene.

geneName

The long description of the target gene.

consSites

The total number of conserved sites.

poorlySites

The total number of poorly conserved sites.

Details

This function sends a miRNA name to the targetscan.org webpage, retrieves the information and gives it back as a data.frame. Options for species are "Human", "Mouse", "Rat", "Chimpanzee", "Rhesus", "Cow", "Dog", "Opossum", "Chicken", "Frog".

References

V. Agarwal, G. Bell, J.Nam, et al. (2015): Predicting effective microRNA target sites in mammalian mRNAs. eLife, 4, pages 1-38, doi: 10.7554/eLife.05005

Examples

# NOT RUN {
targetScan(mirna="miR-9-5p", species="Cow", maxOut=5)
# }