R/xcombr_specificities.R

In wfondrie/xCombR: Identifing crosslinked peptides with standard search engines.

#' Display predefined crosslinker specificities
#'
#' @return A data frame containing details of the predefined crosslinker specificities.
#'
#' @details The data frame returned contains three columns defining the terms for
#' the \code{xlSpecificity} argument of \code{\link{xcombr_db}} and the regular
#' expressions used to find the reaction sites. In these regular expression columns
#' (\code{rxn site 1} and \code{rxn site 2}), the lowercase \code{n} and \code{c}
#' indicate the n-terminus and c-terminus, respectively. The listed regular expressions
#' can be used as a template to define custom specificities using the \code{customSpecificity}
#' argument of \code{\link{xcombr_db}}
#'
#' @examples
#' # Print crosslinker specificities
#' xcombr_specificities()


#' @export xcombr_specificities
#' @include xlinkTbl.R

xcombr_specificities <- function() {
    xlinkTbl %>%
        rename(xlSpecificity = name,
               "rxn site 1" = regex1,
               "rxn site 2" = regex2) %>%
        as.data.frame(.)
}