R/filter_qcov.R

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

#' @title filter_qcov
#' @name filter_qcov
#' @description This function filters BLAST-like tabular output according to
#' percentage query coverage.
#' @param rbh BLAST-like tabular matrix [mandatory]
#' @param qcov query coverage [default: 0.0]
#' @param inverse specify if filter should keep the removed values
#' [default: FALSE]
#' @return rbh matrix
#' @importFrom dplyr filter
#' @examples
#' ## load crbh data
#' data(ath_aly_crbh)
#' dim(ath_aly_crbh$crbh1)
#' dim(filter_qcov(
#'     rbh=ath_aly_crbh$crbh1,
#'     qcov=0.75))
#' @export filter_qcov
#' @author Kristian K Ullrich

filter_qcov <- function(rbh,
    qcov=0.0,
    inverse=FALSE
    ){
    alignment_length <- NULL
    query_length <- NULL
    if(inverse){
        #return(rbh[(as.numeric(rbh[,4])/as.numeric(rbh[,13]))<qcov, ,
        #drop=FALSE])
        return(dplyr::filter(rbh, (alignment_length / query_length)<qcov))
    } else {
        #return(rbh[(as.numeric(rbh[,4])/as.numeric(rbh[,13]))>=qcov, ,
        #drop=FALSE])
        return(dplyr::filter(rbh, (alignment_length / query_length)>=qcov))
    }
}