rfPred-package
(Package: rfPred) :
Assign functional prediction rfPred scores to human missense variants
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...
rfPred_scores
(Package: rfPred) :
Assign functional prediction rfPred scores to human missense variants
rfPred is a statistical method which combines 5 algorithms predictions in a random forest model: SIFT, Polyphen2, LRT, PhyloP and MutationTaster. These scores are available in the dbNFSP database for all the possible missense variants in hg19 version, and the package rfPred gives a composite score more reliable than each of the isolated algorithms.
providing 
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