R/methods-fragments.R

In MSnbase: Base Functions and Classes for Mass Spectrometry and Proteomics

setMethod("calculateFragments", c("character", "missing"),
          function(sequence, type = c("b", "y"), z = 1,
                   modifications = c(C = 57.02146),
                   neutralLoss = defaultNeutralLoss(),
                   verbose = isMSnbaseVerbose()) {
            l <- lapply(sequence, .calculateFragments,
                        type = type, z = z, modifications = modifications,
                        neutralLoss = neutralLoss, verbose = verbose)
            return(do.call(rbind, l))
        })