R: Assign functional prediction rfPred scores to human missense...
rfPred-package
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).