R/filter_rost1999.R

In kullrich/CRBHits: Conditional reciprocal best hits (CRBHits) in R

#' @title filter_rost1999
#' @name filter_rost1999
#' @description This function filters BLAST-like tabular output according to
#' equation 2 of Rost 1999.
#' @param rbh BLAST-like tabular matrix [mandatory]
#' @param inverse specify if filter should keep the removed values
#' [default: FALSE]
#' @return rbh matrix
#' @references Rost B. (1999). Twilight zone of protein sequence alignments.
#' \emph{Protein Engineering}, \bold{12(2)}, 85-94.
#' @examples
#' ## load crbh data
#' data(ath_aly_crbh)
#' dim(ath_aly_crbh$crbh1)
#' dim(filter_rost1999(
#'     rbh=ath_aly_crbh$crbh1))
#' @export filter_rost1999
#' @author Kristian K Ullrich

filter_rost1999 <- function(rbh,
    inverse=FALSE
    ){
    #internal function to calculate pident by length
    get_pident_by_length <- function(x){
        eq2 <- function(x){
            if(x <= 11){return(100)}
            if(x <= 450){return(480*(x^(-0.32*(1+(exp(-x/1000))))))}
            if(x > 450){return(19.5)}
        }
        return(unlist(lapply(x, eq2)))
    }
    pident_by_length <- get_pident_by_length(as.numeric(rbh[, 4]))
    if(inverse){
        return(rbh[as.numeric(rbh[, 3])<pident_by_length, , drop=FALSE])
    } else {
        return(rbh[as.numeric(rbh[, 3])>=pident_by_length, , drop=FALSE])
    }
}