R/filter_alnlen.R

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

#' @title filter_alnlen
#' @name filter_alnlen
#' @description This function filters BLAST-like tabular output according to
#' alignment length.
#' @param rbh BLAST-like tabular matrix [mandatory]
#' @param alnlen alignment length [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$crbh1)
#' dim(filter_alnlen(
#'     rbh=ath_aly_crbh$crbh1,
#'     alnlen=75))
#' @export filter_alnlen
#' @author Kristian K Ullrich

filter_alnlen <- function(rbh,
    alnlen=0.0,
    inverse=FALSE
    ){
    alignment_length <- NULL
    if(inverse){
        #return(rbh[as.numeric(rbh[,4])<alnlen, , drop=FALSE])
        return(dplyr::filter(rbh, .data$alignment_length<alnlen))
    } else {
        #return(rbh[as.numeric(rbh[,4])>=alnlen, , drop=FALSE])
        return(dplyr::filter(rbh, .data$alignment_length>=alnlen))
    }
}