@@ -18,7 +18,7 @@ Description: mzR provides a unified API to the common file formats and

 License: Artistic-2.0

 LazyLoad: yes

 Depends: Rcpp (>= 0.10.1), methods, utils

-Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics

+Imports: Biobase, BiocGenerics (>= 0.13.6), ProtGenerics (>= 1.9.1)

 Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML

 VignetteBuilder: knitr

 LinkingTo: Rcpp, zlibbioc

@@ -13,7 +13,6 @@ export(openMSfile,

        openIDfile,

        pwiz.version,

        nChrom,

-       writeMSData,

        copyWriteMSData)

 exportMethods(close,

@@ -47,7 +46,8 @@ exportMethods(close,

               para,

               tic,

               chromatogram,

-              chromatograms)

+              chromatograms,

+              writeMSData)

 exportClasses("mzR",

               "mzRramp",

@@ -52,45 +52,43 @@ openIDfile <- function(filename, verbose = FALSE) {

                fileName=filename))

 }

-writeMSData <- function(filename, header, data, backend = "pwiz",

-                        outformat = "mzml",

-                        rtime_seconds = TRUE,

-                        software_processing) {

-    backend <- match.arg(backend)

-    ## supp_formats <- c("mzml", "mgf", "mzxml")

-    supp_formats <- c("mzml", "mzxml")

-    outformat <- match.arg(tolower(outformat), supp_formats)

-    if (missing(filename))

-        stop("'filename' is a required parameter")

-    if (missing(header) | missing(data))

-        stop("'header' and 'data' are required")

-    ## Other checks:

-    header <- .validateHeader(header)

-    if (is(header, "character"))

-        stop("Error checking parameter 'header': ", header)

-    is_ok <- .validSpectrumList(data)

-    if (is(is_ok, "character"))

-        stop("Error checking parameter 'data'. First error was: ", is_ok)

-    ## Check software_processing:

-    software_processing <- .check_software_processing(software_processing)

-    ## Add mzR processing:

-    mzR <- c("mzR", paste(packageVersion("mzR"), collapse = "."), "MS:-1")

-    if (outformat == "mzml")

-        mzR <- c(mzR, "MS:1000544")

-    if (outformat == "mzxml")

-        mzR <- c(mzR, "MS:1000545")

-    software_processing <- c(software_processing, list(mzR))

-    if (backend == "pwiz") {

-        if (outformat == "mzxml" & any(header$injectionTime > 0))

-            warning("mzXML export does not support writing ion injection time")

-        pwizModule <- new(Pwiz)

-        pwizModule$writeSpectrumList(filename, outformat,

-                                     header, data, rtime_seconds,

-                                     software_processing)

-    }

-}

+setMethod("writeMSData", signature(object = "list", file = "character"),

+          function(object, file, header, backend = "pwiz",

+                   outformat = "mzml", rtime_seconds = TRUE,

+                   software_processing) {

+              backend <- match.arg(backend)

+              ## supp_formats <- c("mzml", "mgf", "mzxml")

+              supp_formats <- c("mzml", "mzxml")

+              outformat <- match.arg(tolower(outformat), supp_formats)

+              if (missing(header))

+                  stop("'header' is required")

+              ## Other checks:

+              header <- .validateHeader(header)

+              if (is(header, "character"))

+                  stop("Error checking parameter 'header': ", header)

+              is_ok <- .validSpectrumList(object)

+              if (is(is_ok, "character"))

+                  stop("Error checking parameter 'object'. First error was: ", is_ok)

+              ## Check software_processing:

+              software_processing <- .check_software_processing(software_processing)

+              ## Add mzR processing:

+              mzR <- c("mzR", paste(packageVersion("mzR"), collapse = "."), "MS:-1")

+              if (outformat == "mzml")

+                  mzR <- c(mzR, "MS:1000544")

+              if (outformat == "mzxml")

+                  mzR <- c(mzR, "MS:1000545")

+              software_processing <- c(software_processing, list(mzR))

+              if (backend == "pwiz") {

+                  if (outformat == "mzxml" & any(header$injectionTime > 0))

+                      warning("mzXML export does not support writing ion injection time")

+                  pwizModule <- new(Pwiz)

+                  pwizModule$writeSpectrumList(file, outformat,

+                                               header, object, rtime_seconds,

+                                               software_processing)

+              }

+          })

-copyWriteMSData <- function(filename, original_file, header, data,

+copyWriteMSData <- function(object, file, original_file, header,

                             backend = "pwiz",

                             outformat = "mzml",

                             rtime_seconds = TRUE,

@@ -99,21 +97,21 @@ copyWriteMSData <- function(filename, original_file, header, data,

     ## supp_formats <- c("mzml", "mgf", "mzxml")

     supp_formats <- c("mzml", "mzxml")

     outformat <- match.arg(tolower(outformat), supp_formats)

-    if (missing(filename))

-        stop("'filename' is a required parameter")

+    if (missing(file))

+        stop("'file' is a required parameter")

     if (missing(original_file))

         stop("'original_file' is a required parameter")

-    if (missing(header) | missing(data))

-        stop("'header' and 'data' are required")

+    if (missing(header) | missing(object))

+        stop("'header' and 'object' are required")

     if (!file.exists(original_file))

         stop("Original file ", original_file, " not found")

     ## Other checks:

     header <- .validateHeader(header)

     if (is(header, "character"))

         stop("Error checking parameter 'header': ", header)

-    is_ok <- .validSpectrumList(data)

+    is_ok <- .validSpectrumList(object)

     if (is(is_ok, "character"))

-        stop("Error checking parameter 'data'. First error was: ", is_ok)

+        stop("Error checking parameter 'object'. First error was: ", is_ok)

     ## Check software_processing:

     software_processing <- .check_software_processing(software_processing)

     ## Add mzR processing:

@@ -129,8 +127,8 @@ copyWriteMSData <- function(filename, original_file, header, data,

             header$injectionTime = 0

         }

         pwizModule <- new(Pwiz)

-        pwizModule$copyWriteMSfile(filename, outformat, original_file,

-                                   header, data, rtime_seconds,

+        pwizModule$copyWriteMSfile(file, outformat, original_file,

+                                   header, object, rtime_seconds,

                                    software_processing)

     }

 }

@@ -8,7 +8,7 @@ test_copyWriteMSData <- function() {

     ## INPUT: mzXML

     orig_file <- system.file("threonine", "threonine_i2_e35_pH_tree.mzXML",

-                        package = "msdata")

+                             package = "msdata")

     mzxml <- openMSfile(orig_file, backend = "pwiz")

     pks <- peaks(mzxml)

     hdr <- header(mzxml)

@@ -17,8 +17,8 @@ test_copyWriteMSData <- function() {

     ## OUTPUT: mzML

     fnew <- paste0(test_folder, "test_copyWrite.mzML")

-    mzR:::copyWriteMSData(filename = fnew, original_file = orig_file,

-                          header = hdr, data = pks, backend = "pwiz")

+    mzR::copyWriteMSData(file = fnew, original_file = orig_file,

+                         header = hdr, object = pks, backend = "pwiz")

     ## Check content is same

     mzml_new <- openMSfile(fnew, backend = "pwiz")

     pks_new <- peaks(mzml_new)

@@ -31,9 +31,9 @@ test_copyWriteMSData <- function() {

     ## OUTPUT: mzXML

     fnew <- paste0(test_folder, "test_copyWrite.mzXML")

-    mzR:::copyWriteMSData(filename = fnew, original_file = orig_file,

-                          header = hdr, data = pks, backend = "pwiz",

-                          outformat = "mzxml")

+    mzR::copyWriteMSData(file = fnew, original_file = orig_file,

+                         header = hdr, object = pks, backend = "pwiz",

+                         outformat = "mzxml")

     ## Check content is same

     mzml_new <- openMSfile(fnew, backend = "pwiz")

     pks_new <- peaks(mzml_new)

@@ -64,15 +64,15 @@ test_copyWriteMSData <- function() {

     pks_sub <- pks[c(1, 3, 5)]

     fnew <- paste0(test_folder, "test_copyWrite.mzML")

     ## index is not OK after subsetting

-    checkException(mzR:::copyWriteMSData(filename = fnew,

+    checkException(mzR:::copyWriteMSData(file = fnew,

                                          original_file = orig_file,

-                                         header = hdr_sub, data = pks_sub,

+                                         header = hdr_sub, object = pks_sub,

                                          backend = "pwiz"))

     hdr_sub$seqNum <- seq_len(nrow(hdr_sub))

     ## mzML

-    mzR:::copyWriteMSData(filename = fnew, original_file = orig_file,

-                          header = hdr_sub, data = pks_sub, backend = "pwiz",

-                          outformat = "mzml")

+    mzR::copyWriteMSData(file = fnew, original_file = orig_file,

+                         header = hdr_sub, object = pks_sub, backend = "pwiz",

+                         outformat = "mzml")

     ## Check content is same

     mzml_new <- openMSfile(fnew, backend = "pwiz")

     pks_new <- peaks(mzml_new)

@@ -83,9 +83,9 @@ test_copyWriteMSData <- function() {

     checkEquals(pks_new, pks_sub)

     checkEquals(hdr_new, hdr_sub)

     ## mzXML

-    mzR:::copyWriteMSData(filename = fnew, original_file = orig_file,

-                          header = hdr_sub, data = pks_sub, backend = "pwiz",

-                          outformat = "mzxml")

+    mzR::copyWriteMSData(file = fnew, original_file = orig_file,

+                         header = hdr_sub, object = pks_sub, backend = "pwiz",

+                         outformat = "mzxml")

     ## Check content is same

     mzml_new <- openMSfile(fnew, backend = "pwiz")

     pks_new <- peaks(mzml_new)

@@ -108,27 +108,27 @@ test_copyWriteMSData <- function() {

     ## wrong header.

     ## wrong spectra.

     ## wrong data processing.

-    checkException(mzR:::copyWriteMSData(filename = fnew,

-                                         original_file = orig_file,

-                                         header = pks, data = hdr,

-                                         backend = "pwiz"))

-    checkException(mzR:::copyWriteMSData(filename = fnew,

-                                         original_file = orig_file,

-                                         header = hdr, data = hdr,

-                                         backend = "pwiz"))

-    checkException(mzR:::copyWriteMSData(filename = fnew,

-                                         original_file = orig_file,

-                                         header = hdr, data = pks,

-                                         backend = "Ramp"))

-    checkException(mzR:::copyWriteMSData(filename = fnew,

-                                         original_file = "somefile",

-                                         header = hdr, data = pks,

-                                         backend = "pwiz"))

-    checkException(mzR:::copyWriteMSData(filename = fnew,

-                                         original_file = orig_file,

-                                         header = hdr, data = pks,

-                                         backend = "pwiz",

-                                         software_processing = c("other")))

+    checkException(mzR::copyWriteMSData(file = fnew,

+                                        original_file = orig_file,

+                                        header = pks, object = hdr,

+                                        backend = "pwiz"))

+    checkException(mzR::copyWriteMSData(file = fnew,

+                                        original_file = orig_file,

+                                        header = hdr, object = hdr,

+                                        backend = "pwiz"))

+    checkException(mzR::copyWriteMSData(file = fnew,

+                                        original_file = orig_file,

+                                        header = hdr, object = pks,

+                                        backend = "Ramp"))

+    checkException(mzR::copyWriteMSData(file = fnew,

+                                        original_file = "somefile",

+                                        header = hdr, object = pks,

+                                        backend = "pwiz"))

+    checkException(mzR::copyWriteMSData(file = fnew,

+                                        original_file = orig_file,

+                                        header = hdr, object = pks,

+                                        backend = "pwiz",

+                                        software_processing = c("other")))

     ## INPUT: mzML

     orig_file <- system.file("proteomics",

@@ -142,8 +142,8 @@ test_copyWriteMSData <- function() {

     ## OUTPUT: mzML

     fnew <- paste0(test_folder, "test_copyWrite.mzML")

-    mzR:::copyWriteMSData(filename = fnew, original_file = orig_file,

-                          header = hdr, data = pks, backend = "pwiz")

+    mzR::copyWriteMSData(file = fnew, original_file = orig_file,

+                         header = hdr, object = pks, backend = "pwiz")

     ## Check content is same

     mzml_new <- openMSfile(fnew, backend = "pwiz")

     pks_new <- peaks(mzml_new)

@@ -156,9 +156,9 @@ test_copyWriteMSData <- function() {

     ## OUTPUT: mzXML

     fnew <- paste0(test_folder, "test_copyWrite.mzXML")

-    mzR:::copyWriteMSData(filename = fnew, original_file = orig_file,

-                          header = hdr, data = pks, backend = "pwiz",

-                          outformat = "mzxml")

+    mzR::copyWriteMSData(file = fnew, original_file = orig_file,

+                         header = hdr, object = pks, backend = "pwiz",

+                         outformat = "mzxml")

     ## Check content is same

     mzml_new <- openMSfile(fnew, backend = "pwiz")

     pks_new <- peaks(mzml_new)

@@ -194,9 +194,9 @@ test_copyWriteMSData <- function() {

     pks_sub <- pks[idx]

     hdr_sub$seqNum <- 1:nrow(hdr_sub)

     fnew <- paste0(test_folder, "test_copyWrite.mzML")

-    mzR:::copyWriteMSData(filename = fnew, original_file = orig_file,

-                          header = hdr_sub, data = pks_sub, backend = "pwiz",

-                          outformat = "mzml")

+    mzR::copyWriteMSData(file = fnew, original_file = orig_file,

+                         header = hdr_sub, object = pks_sub, backend = "pwiz",

+                         outformat = "mzml")

     ## Check content is same

     mzml_new <- openMSfile(fnew, backend = "pwiz")

     pks_new <- peaks(mzml_new)

@@ -211,9 +211,9 @@ test_copyWriteMSData <- function() {

     ## Subset with mzXML

     fnew <- paste0(test_folder, "test_copyWrite.mzXML")

-    mzR:::copyWriteMSData(filename = fnew, original_file = orig_file,

-                          header = hdr_sub, data = pks_sub, backend = "pwiz",

-                          outformat = "mzxml")

+    mzR::copyWriteMSData(file = fnew, original_file = orig_file,

+                         header = hdr_sub, object = pks_sub, backend = "pwiz",

+                         outformat = "mzxml")

     ## Check content is same

     mzml_new <- openMSfile(fnew, backend = "pwiz")

     pks_new <- peaks(mzml_new)

@@ -244,9 +244,9 @@ test_copyWriteMSData <- function() {

     ## mzML

     out_file <- paste0(test_folder, "test_copyWrite.mzML")

-    mzR:::copyWriteMSData(filename = out_file, original_file = test_file,

-                          header = hdr, data = pks,

-                          software_processing = c("MSnbase", "2.3.8"))

+    mzR::copyWriteMSData(file = out_file, original_file = test_file,

+                         header = hdr, object = pks,

+                         software_processing = c("MSnbase", "2.3.8"))

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -258,9 +258,9 @@ test_copyWriteMSData <- function() {

     ## mzXML output:

     out_file <- paste0(test_folder, "test_copyWrite.mzXML")

-    mzR:::copyWriteMSData(filename = out_file, original_file = test_file,

-                          header = hdr, data = pks, outformat = "mzXML",

-                          software_processing = c("MSnbase", "2.3.8"))

+    mzR::copyWriteMSData(file = out_file, original_file = test_file,

+                         header = hdr, object = pks, outformat = "mzXML",

+                         software_processing = c("MSnbase", "2.3.8"))

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -287,7 +287,7 @@ test_writeMSData <- function() {

     ## mzML

     out_file <- paste0(test_folder, "test_write.mzML")

-    mzR:::writeMSData(filename = out_file, header = hdr, data = pks)

+    writeMSData(file = out_file, header = hdr, object = pks)

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -299,7 +299,7 @@ test_writeMSData <- function() {

     hdr_sub <- hdr[c(1, 3, 5), ]

     hdr_sub$seqNum <- 1:nrow(hdr_sub)

     pks_sub <- pks[c(1, 3, 5)]

-    mzR:::writeMSData(out_file, header = hdr_sub, data = pks_sub)

+    writeMSData(pks_sub, out_file, header = hdr_sub)

     in_file <- openMSfile(out_file)

     hdr_sub_2 <- header(in_file)

     pks_sub_2 <- peaks(in_file)

@@ -319,8 +319,8 @@ test_writeMSData <- function() {

     ## mzXML output:

     out_file <- paste0(test_folder, "test_write.mzXML")

-    mzR:::writeMSData(filename = out_file, header = hdr, data = pks,

-                      outformat = "mzXML")

+    writeMSData(file = out_file, header = hdr, object = pks,

+                outformat = "mzXML")

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -331,8 +331,8 @@ test_writeMSData <- function() {

     hdr_sub <- hdr[c(1, 3, 5), ]

     hdr_sub$seqNum <- 1:nrow(hdr_sub)

     pks_sub <- pks[c(1, 3, 5)]

-    mzR:::writeMSData(out_file, header = hdr_sub, data = pks_sub,

-                      outformat = "mzXML")

+    writeMSData(file = out_file, header = hdr_sub, object = pks_sub,

+                outformat = "mzXML")

     in_file <- openMSfile(out_file)

     hdr_sub_2 <- header(in_file)

     pks_sub_2 <- peaks(in_file)

@@ -373,7 +373,7 @@ test_writeMSData <- function() {

     ## mzML

     out_file <- paste0(test_folder, "test_write.mzML")

-    mzR:::writeMSData(filename = out_file, header = hdr, data = pks)

+    writeMSData(pks, file = out_file, header = hdr)

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -390,8 +390,8 @@ test_writeMSData <- function() {

     ## mzXML output:

     out_file <- paste0(test_folder, "test_write.mzXML")

-    mzR:::writeMSData(filename = out_file, header = hdr, data = pks,

-                      outformat = "mzXML")

+    writeMSData(file = out_file, header = hdr, object = pks,

+                outformat = "mzXML")

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -424,9 +424,9 @@ test_writeMSData <- function() {

     hdr_sub$seqNum <- 1:nrow(hdr_sub)

     pks_sub <- pks[idx]

     fnew <- paste0(test_folder, "test_copyWrite.mzML")

-    mzR:::writeMSData(filename = fnew,

-                      header = hdr_sub, data = pks_sub, backend = "pwiz",

-                      outformat = "mzml")

+    writeMSData(file = fnew,

+                header = hdr_sub, object = pks_sub, backend = "pwiz",

+                outformat = "mzml")

     ## Check content is same

     mzml_new <- openMSfile(fnew, backend = "pwiz")

     pks_new <- peaks(mzml_new)

@@ -450,8 +450,8 @@ test_writeMSData <- function() {

     hdr_sub$seqNum <- 1:nrow(hdr_sub)

     pks_sub <- pks[idx]

     fnew <- paste0(test_folder, "test_copyWrite.mzXML")

-    mzR:::writeMSData(filename = fnew, header = hdr_sub, data = pks_sub,

-                      backend = "pwiz", outformat = "mzxml")

+    writeMSData(file = fnew, header = hdr_sub, object = pks_sub,

+                backend = "pwiz", outformat = "mzxml")

     ## Check content is same

     mzml_new <- openMSfile(fnew, backend = "pwiz")

     pks_new <- peaks(mzml_new)

@@ -482,7 +482,7 @@ test_writeMSData <- function() {

     ## mzML

     out_file <- paste0(test_folder, "test_write.mzML")

-    mzR:::writeMSData(filename = out_file, header = hdr, data = pks)

+    writeMSData(file = out_file, header = hdr, object = pks)

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -492,8 +492,8 @@ test_writeMSData <- function() {

     ## mzXML output:

     out_file <- paste0(test_folder, "test_write.mzXML")

-    mzR:::writeMSData(filename = out_file, header = hdr, data = pks,

-                      outformat = "mzXML")

+    writeMSData(file = out_file, header = hdr, object = pks,

+                outformat = "mzXML")

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -511,7 +511,7 @@ test_writeMSData <- function() {

     ## mzML

     out_file <- paste0(test_folder, "test_write.mzML")

-    mzR:::writeMSData(filename = out_file, header = hdr, data = pks)

+    writeMSData(file = out_file, header = hdr, object = pks)

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -521,8 +521,8 @@ test_writeMSData <- function() {

     ## mzXML output:

     out_file <- paste0(test_folder, "test_write.mzXML")

-    mzR:::writeMSData(filename = out_file, header = hdr, data = pks,

-                      outformat = "mzXML")

+    writeMSData(file = out_file, header = hdr, object = pks,

+                outformat = "mzXML")

     in_file <- openMSfile(out_file, backend = "pwiz")

     hdr_2 <- header(in_file)

     pks_2 <- peaks(in_file)

@@ -7,12 +7,20 @@

 }

 \usage{

-  copyWriteMSData(filename, original_file, header, data, backend =

+  copyWriteMSData(object, file, original_file, header, backend =

     "pwiz", outformat = "mzml", rtime_seconds = TRUE, software_processing)

 }

 \arguments{

-  \item{filename}{

+  

+  \item{object}{

+    \code{list} containing for each spectrum one \code{matrix} with

+    columns \code{mz} (first column) and \code{intensity} (second

+    column). See also \code{\link{peaks}} for the method that reads such

+    data from an MS file.

+  }

+

+  \item{file}{

     \code{character(1)} defining the name of the file.

   }

@@ -26,14 +34,7 @@

     the format as the \code{data.frame} returned by the

     \code{\link{header}} method.

   }

-  

-  \item{data}{

-    \code{list} containing for each spectrum one \code{matrix} with

-    columns \code{mz} (first column) and \code{intensity} (second

-    column). See also \code{\link{peaks}} for the method that reads such

-    data from an MS file.

-  }

-  

+    

   \item{backend}{

     \code{character(1)} defining the backend that should be used for

     writing. Currently only \code{"pwiz"} backend is supported.

@@ -113,6 +114,6 @@ pks <- lapply(pks, function(z) {

 ## Copy metadata and additional information from the originating file

 ## and save it, along with the modified data, to a new mzML file.

 out_file <- tempfile()

-copyWriteMSData(filename = out_file, original_file = fl,

-    header = hdr, data = pks)

+copyWriteMSData(pks, file = out_file, original_file = fl,

+    header = hdr)

 }

@@ -1,15 +1,24 @@

 \name{writeMSData}

 \alias{writeMSData}

+\alias{writeMSData,list,character-method}

 \title{

   Write MS spectrum data to an MS file

 }

 \usage{

-writeMSData(filename, header, data, backend = "pwiz", outformat =

-   "mzml", rtime_seconds = TRUE, software_processing)

+

+\S4method{writeMSData}{list,character}(object, file, header,

+    backend = "pwiz", outformat = "mzml", rtime_seconds = TRUE,

+    software_processing)

 }

 \arguments{

-  \item{filename}{

+  \item{object}{

+    \code{list} containing for each spectrum one \code{matrix} with

+    columns \code{mz} (first column) and \code{intensity} (second

+    column). See also \code{\link{peaks}} for the method that reads such

+    data from an MS file.

+  }

+  \item{file}{

     \code{character(1)} defining the name of the file.

   }

   \item{header}{

@@ -17,12 +26,6 @@ writeMSData(filename, header, data, backend = "pwiz", outformat =

     the format as the \code{data.frame} returned by the

     \code{\link{header}} method.

   }

-  \item{data}{

-    \code{list} containing for each spectrum one \code{matrix} with

-    columns \code{mz} (first column) and \code{intensity} (second

-    column). See also \code{\link{peaks}} for the method that reads such

-    data from an MS file.

-  }

   \item{backend}{

     \code{character(1)} defining the backend that should be used for

     writing. Currently only \code{"pwiz"} backend is supported.

@@ -84,5 +87,5 @@ pks <- lapply(pks, function(z) {

 ## Write the data to a mzML file.

 out_file <- tempfile()

-writeMSData(filename = out_file, header = hdr, data = pks)

+writeMSData(object = pks, file = out_file, header = hdr)

 }