rfPred-package {rfPred} | R Documentation

## Assign functional prediction rfPred scores to human missense variants (random forest method based on SIFT, Polyphen2, PhyloP, LRT and Mutation Taster)

### Description

The package provides a function which returns the rfPred score for a list of non-synonymous missense variants. All the rfPred scores are pre-calculated and stored in a `TabixFile` available on a server and which can be downloaded for using the package while not connected on the Internet. The package does not work without an access to the `TabixFile`. However, a toy example on the chromosome Y is available within the package to test the `rfPred_scores` function. curves with numbers of subjects at risk, compare data sets, display spaghetti-plot, build multi-contingency tables...

### Author(s)

Fabienne Jabot-Hanin, Hugo Varet and Jean-Philippe Jais

### References

dbNSFP database: Liu X, Jian X and Boerwinkle E. 2011. dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions. Human Mutation. 32:894-899.

rfPred method: Jabot-Hanin F, Varet H, Tores F and Jais J-P. 2013. rfPred: a new meta-score for functional prediction of missense variants in human exome (submitted).

[Package rfPred version 1.22.0 Index]