targetScan: Retrieving miRNA target information from targetscan.org

In fischuu/hoardeR: Collect and Retrieve Annotation Data for Various Genomic Data Using Different Webservices

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.

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".

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.

Author(s)

Daniel Fischer

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)

## End(Not run)

fischuu/hoardeR documentation built on April 13, 2024, 1:20 p.m.