@@ -2,18 +2,18 @@ Package: mzR

 Type: Package

 Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files

        (mass spectrometry data)

-Version: 2.17.3

+Version: 2.17.4

 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer

 Maintainer: Steffen Neumann <sneumann@ipb-halle.de>,

 	    Laurent Gatto <lg390@cam.ac.uk>,

 	    Qiang Kou <qkou@umail.iu.edu>

 Description: mzR provides a unified API to the common file formats and

-        parsers available for mass spectrometry data. It comes with a

-        wrapper for the ISB random access parser for mass spectrometry

-        mzXML, mzData and mzML files. The package contains the

-        original code written by the ISB, and a subset of the

-        proteowizard library for mzML and mzIdentML. The netCDF

-        reading code has previously been used in XCMS.

+	parsers available for mass spectrometry data. It comes with a

+	wrapper for the ISB random access parser for mass spectrometry

+	mzXML, mzData and mzML files. The package contains the

+	original code written by the ISB, and a subset of the

+	proteowizard library for mzML and mzIdentML. The netCDF

+	reading code has previously been used in XCMS.

 License: Artistic-2.0

 LazyLoad: yes

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

@@ -26,5 +26,5 @@ SystemRequirements: C++11, GNU make

 URL: https://github.com/sneumann/mzR/

 BugReports: https://github.com/sneumann/mzR/issues/

 biocViews: ImmunoOncology, Infrastructure, DataImport, Proteomics, Metabolomics,

-        MassSpectrometry

+	MassSpectrometry

 RoxygenNote: 6.0.1

@@ -1,3 +1,8 @@

+CHANGES IN VERSION 2.17.4

+-------------------------

+ o Update documentation, pointing to MSnbase rather than directly use

+   low-level classes. <2019-04-17 Wed>

+

 CHANGES IN VERSION 2.17.3

 -------------------------

  o Extract isolation window from mzML files (issue #193): data.frame returned

@@ -14,9 +19,9 @@ CHANGES IN VERSION 2.15.5

 CHANGES IN VERSION 2.15.4

 -------------------------

- o Use new dependency ncdf4 for netCDF reading, 

+ o Use new dependency ncdf4 for netCDF reading,

    removes a lot of build hassles with old libnetcdf-dev linking.

- o specParams returns a numeric scan.number.s. 

+ o specParams returns a numeric scan.number.s.

 CHANGES IN VERSION 2.15.3

 -------------------------

@@ -75,10 +75,19 @@

   \code{mzRpwiz} are available implementations. \code{mzRramp} uses the

   ISB 'RAMP' random access C/C++ API, and \code{mzRpwiz} uses

   Proteowizard to access the relevant information in \code{mzData},

-  \code{mzXML} and \code{mzML} files. 

+  \code{mzXML} and \code{mzML} files. \code{mzRident} is used as an

+  interface to \code{mzIdentML} files.

+

+  IMPORTANT: New developers that need to access and manipulate raw mass

+  spectrometry data are advised against using this infrastucture

+  directly. They are invited to use the corresponding \code{MSnExp}

+  (with \emph{on disk} mode) from the MSnbase package instead. The

+  latter supports reading multiple files at once and offers access to

+  the spectra data (m/z and intensity) as well as all the spectra

+  metadata using a coherent interface. The MSnbase infrastructure itself

+  used the low level classes in mzR, thus offering fast and efficient

+  access.

-  Additional sub-classes using the proteowizard API and netCDF are

-  planned.

 }

 \section{Objects from the Class}{

@@ -86,10 +95,11 @@

   Objects can be created by calls of the form \code{new("mzRramp",

     ...)}, but more often they will be created with

-  \code{\link{openMSfile}}.  

-  

-  After creating a \code{mzR}, you can write it into a file.

-  mzXML, mzML, mgf formats are supported. 

+  \code{\link{openMSfile}}.

+

+  After creating an \code{mzR} object, one can write it into a new file.

+  mzXML, mzML, mgf formats are supported.

+

 }

 \section{Slots}{

@@ -102,6 +112,7 @@

       from Biobase.}

   }

 }

+

 \section{Extends}{

   Class \code{"\linkS4class{Versioned}"}, directly.

 }

@@ -110,14 +121,14 @@

   For methods to access raw data (spectra and chromatograms), see

   \code{\link{peaks}}.

-  

-  

+

+

   Methods currently implemented for \code{mzR}

   \describe{ \item{fileName}{\code{signature(object = "mzR")}: ... } }

-  

+

   Methods currently implemented for \code{mzRramp}

-  

+

   \describe{

     \item{analyzer}{\code{signature(object = "mzRramp")}: ... }

     \item{close}{\code{signature(con = "mzRramp")}: ... }

@@ -145,7 +156,7 @@

     \item{runInfo}{\code{signature(object = "mzRpwiz")}: ... }

     \item{chromatogramsInfo}{\code{signature(object = "mzRpwiz")}: ... }

   }

-  

+

   Methods currently implemented for \code{mzRident}

   \describe{

     \item{mzidInfo}{\code{signature(object = "mzRident")}: ... }

@@ -175,7 +186,7 @@

  library(msdata)

  filepath <- system.file("microtofq", package = "msdata")

  file <- list.files(filepath, pattern="MM14.mzML",

-                     full.names=TRUE, recursive = TRUE)

+		     full.names=TRUE, recursive = TRUE)

  mzml <- openMSfile(file)

  close(mzml)

@@ -1,6 +1,6 @@

 ---

 title: "A parser for raw and identification mass-spectrometry data"

-author: 

+author:

 - name: Bernd Fischer

 - name: Steffen Neumann

 - name: Laurent Gatto

@@ -9,7 +9,7 @@ package: mzR

 output:

   BiocStyle::html_document:

     toc_float: true

-bibliography: mzR.bib 	

+bibliography: mzR.bib

 vignette: >

   %\VignetteEngine{knitr::rmarkdown}

   %\VignetteIndexEntry{Accessin raw mass spectrometry and identification data}

@@ -26,7 +26,7 @@ interface to several mass spectrometry data formats, namely `mzData`

 data, and `mzIdentML` [@Jones2012], somewhat similar to the

 Bioconductor package affyio for affymetrix raw data. No processing is

 done in `r BiocStyle::Biocpkg("mzR")`, which is left to packages such as `r

-BiocStyle::Biocpkg("xcms")` [@Smith:2006, Tautenhahn:2008] or 

+BiocStyle::Biocpkg("xcms")` [@Smith:2006, Tautenhahn:2008] or

 `r BiocStyle::Biocpkg("MSnbase")` [@Gatto:2012]. These packages also provide more

 convenient, high-level interfaces to raw and identification. data

@@ -55,6 +55,16 @@ The `r BiocStyle::Biocpkg("mzR")` package is in essence a collection of wrappers

 to the C++ code, and benefits from the C++ interface provided through

 the Rcpp package [@Rcpp11].

+**IMPORTANT** New developers that need to access and manipulate raw

+mass spectrometry data are advised against using this infrastucture

+directly. They are invited to use the corresponding `MSnExp` (with *on

+disk* mode) from the`r BiocStyle::Biocpkg("MSnbase")` package instead. The

+latter supports reading multiple files at once and offers access to

+the spectra data (m/z and intensity) as well as all the spectra

+metadata using a coherent interface. The MSnbase infrastructure itself

+used the low level classes in mzR, thus offering fast and efficient

+access.

+

 # Mass spectrometry raw data

@@ -107,17 +117,17 @@ depends on the MS software which converted the data.

 ## `mzXML`/`mzML`/`mzData` files

-A short example sequence to read data from a mass spectrometer. 

+A short example sequence to read data from a mass spectrometer.

 First open the file.

 ```{r openraw}

 library(mzR)

 library(msdata)

-mzxml <- system.file("threonine/threonine_i2_e35_pH_tree.mzXML", 

+mzxml <- system.file("threonine/threonine_i2_e35_pH_tree.mzXML",

                      package = "msdata")

-aa <- openMSfile(mzxml) 

-``` 

+aa <- openMSfile(mzxml)

+```

 We can obtain different kind of header information.

@@ -125,7 +135,7 @@ We can obtain different kind of header information.

 runInfo(aa)

 instrumentInfo(aa)

 header(aa,1)

-``` 

+```

 Read a single spectrum from the file.

@@ -134,14 +144,14 @@ pl <- peaks(aa,10)

 peaksCount(aa,10)

 head(pl)

 plot(pl[,1], pl[,2], type="h", lwd=1)

-``` 

+```

 One should always close the file when not needed any more. This will

 release the memory of cached content.

 ```{r close the file}

 close(aa)

-``` 

+```

 ## `mzIdentML` files

@@ -154,14 +164,14 @@ library(msdata)

 file <- system.file("mzid", "Tandem.mzid.gz", package="msdata")

 x <- openIDfile(file)

-``` 

+```

 `mzidInfo` function will return general information about this

 identification result.

 ```{r metadata}

 mzidInfo(x)

-``` 

+```

 `psms` will return the detailed information on each

 peptide-spectrum-match, include `spectrumID`, `chargeState`,

@@ -196,8 +206,8 @@ colnames(scr)

 Other file formats provided by HUPO, such as `mzQuantML` for

 quantitative data [@Walzer:2013] are also possible in the future.

-# Session information {#sec:sessionInfo} 

+# Session information {#sec:sessionInfo}

 ```{r label=sessioninfo, results='asis', echo=FALSE}

 toLatex(sessionInfo())

-``` 

+```