R/rfPred-package.r

In rfPred: Assign rfPred functional prediction scores to a missense variants list

#' 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 \code{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 \code{TabixFile}. However, a toy example on the 
#' chromosome Y is available within the package to test the \code{rfPred_scores} function.
#' curves with numbers of subjects at risk, compare data sets, display spaghetti-plot, build multi-contingency tables...
#' @title Assign functional prediction rfPred scores to human missense variants 
#' (random forest method based on SIFT, Polyphen2, PhyloP, LRT and Mutation Taster)
#' @author Fabienne Jabot-Hanin, Hugo Varet and Jean-Philippe Jais
#' @docType package
#' @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).
#' @name rfPred-package
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