#' @include xcombr_db-generic.R xcombr_db.R
#'
#' @param x An \code{\link[Biostrings]{AAStringSet}} or \code{\link[Biostrings]{AAString}}
#' @param xlSpecificity Defines the crosslinker specificity. Case insensitive.
#' @param linkType Should intra and/or inter-protein crosslinks be considered?
#' Must be either \code{"intra"}, \code{"inter"}, or \code{"both"}
#' @param minLength Minimum peptide length for either of the crosslinked
#' peptides.
#' @param maxLength Maximum peptide length for either of the crosslinked
#' peptides.
#' @param peptideTerminalLink Should crosslinks at terminal residues of peptides
#' be considered?
#' @param proteinTerminalLink Should crosslinks at terminal residues of the proteins
#' be considered?
#' @param customSpecificity Optional. Used if \code{xlSpecificity = "custom"}.
#' Must be a character vector of length 2 containing regular expressions for specificity rules.
#' @param digest Locgical indicating the whether the input AAStringSet or AAString should be
#' digested using \code{\link[cleaver]{cleave}}.
#' @param ... Arguments passed to \code{\link[cleaver]{cleave}} to indicate digestion
#' settings.
#' @param max50 Limits the maximum number of proteins to 50.
#'
#' @value An \code{\link[Biostrings]{AAStringSet}} of peptide sequences generated using
#' the xComb algorithm.
#'
#' @rdname xcombr_db
setMethod(f="xcombr_db",
signature=signature(x="AAString"),
definition=function(x,
xlSpecificity = "Amine:Amine",
linkType = "both",
minLength = 6,
maxLength = 24,
peptideTerminalLink = FALSE,
proteinTerminalLink = TRUE,
customSpecificity = NULL,
digest = T,
...,
max50 = TRUE) {
x <- AAStringSet(x)
names(x) <- "Sequence_1"
.xcombr_db(x,
xlSpecificity = xlSpecificity,
linkType = linkType,
minLength = minLength,
maxLength = maxLength,
peptideTerminalLink = peptideTerminalLink,
proteinTerminalLink = proteinTerminalLink,
customSpecificity = customSpecificity,
digest = digest,
...,
max50 = max50)
})
#' @rdname xcombr_db
setMethod(f="xcombr_db",
signature=signature(x="AAStringSet"),
definition=function(x,
xlSpecificity = "Amine:Amine",
linkType = "both",
minLength = 6,
maxLength = 24,
peptideTerminalLink = FALSE,
proteinTerminalLink = TRUE,
cleavageRanges = NULL,
customSpecificity = NULL,
digest = T,
...,
max50 = TRUE) {
if(is.null(names(x))) {
names(x) <- paste0("Sequence_", 1:length(x))
}
.xcombr_db(x,
xlSpecificity = xlSpecificity,
linkType = linkType,
minLength = minLength,
maxLength = maxLength,
peptideTerminalLink = peptideTerminalLink,
proteinTerminalLink = proteinTerminalLink,
customSpecificity = customSpecificity,
digest = digest,
...,
max50 = max50)
})
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