get_mirecords: Get predicted and validated targets for miRNAs using...

Description Usage Arguments Value Author(s) References Examples

Description

miRecords (http://c1.accurascience.com/miRecords/) is a resource for animal miRNA-target interactions. There are two components in miRecords. The experimentally Validated Targets (vt) component and the Predicted Targets (pt) component which is an integration of predicted miRNA targets produced by 11 established miRNA target prediction programs.

Usage

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get_mirecords_pt(miRNAs, n = 5, species = "Homo sapiens",
  result_file = "mirna_mirecords_predicted_targets.txt",
  keep_db_names = FALSE, show_progress = TRUE)

get_mirecords_vt(miRNAs, species = "Homo sapiens", version = 4)

Arguments

miRNAs

a character vector containing miRNA names (e.g.: miRNAs = c("hsa-miR-16", "hsa-miR-34a))

n

integer specifying the minimal number of prediction for each miRNA. In other words, Only predicted target by at least n/11 database are kept. Default value is 5.

species

species names as available on miRecords database. Possible values are one of: "Homo sapiens", "Mus musculus", "Rattus norvegicus", "Caenorhabditis elegans", "Drosophila melanogaster", "Gallus gallus", "Ovis aries", "Canis familiaris". Default value is "Homo sapiens".

result_file

path to result file for holding miRNA predicted/validated targets. Default values are "mirna_mirecords_predicted_targets.txt".

keep_db_names

logical value. If TRUE, keep the name of the 11 databases used for target predictions.

show_progress

logical value. If TRUE, a progress bar is shown.

version

miRecords version. Default value is 4

Value

Author(s)

Alboukadel Kassambara [email protected]

References

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

Examples

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## Not run: 
# Predicted targets
 ptget <- get_mirecords_pt(c("hsa-miR-16", "hsa-miR-155"))
 head(ptget)

# Validated targets
 vtget <- get_mirecords_vt(c("hsa-miR-16", "hsa-miR-155"))
 head(vtget)


## End(Not run)

kassambara/miRTarget documentation built on May 18, 2017, 4:15 p.m.