diff --git a/DESCRIPTION b/DESCRIPTION index 34d2be3c9..588d5f5fb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mzR Type: Package -Title: parser for netCDF, mzXML, mzData and mzML and mzIdentML files +Title: parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data) -Version: 2.37.1 +Version: 2.37.2 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer Authors@R: c( person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")), @@ -12,8 +12,8 @@ Authors@R: c( ) Description: mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a - subset of the proteowizard library for mzXML, mzML and mzIdentML. The netCDF - reading code has previously been used in XCMS. + subset of the proteowizard library for mzXML, mzML and mzIdentML. + The netCDF reading code has previously been used in XCMS. License: Artistic-2.0 LazyLoad: yes Depends: diff --git a/NEWS b/NEWS index f3d334624..c52a19193 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,8 @@ +CHANGES IN VERSION 2.37.2 +------------------------- +o remove mentions of mzData in the DESCRIPTION, vignette and manual + files (support dropped in 2.29.3) + CHANGES IN VERSION 2.37.1 ------------------------- o fix compilation on centOS 7 / R-4.3.1 reported in #286 diff --git a/man/mzR-class.Rd b/man/mzR-class.Rd index 337d12969..8fba3cf3f 100644 --- a/man/mzR-class.Rd +++ b/man/mzR-class.Rd @@ -59,8 +59,7 @@ The sub-classes implement specific APIs to access the underlying data and metadata in the files. Currently \code{mzRpwiz} is available. - \code{mzRpwiz} uses - Proteowizard to access the relevant information in \code{mzData}, + \code{mzRpwiz} uses Proteowizard to access the relevant information in \code{mzXML} and \code{mzML} files. \code{mzRident} is used as an interface to \code{mzIdentML} files. @@ -154,7 +153,7 @@ 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) diff --git a/man/openMSfile.Rd b/man/openMSfile.Rd index 822dbac05..bd8c81d4a 100644 --- a/man/openMSfile.Rd +++ b/man/openMSfile.Rd @@ -5,7 +5,7 @@ \alias{openIDfile} \title{ - Create and check mzR objects from netCDF, mzXML, mzData or mzML files. + Create and check mzR objects from netCDF, mzXML or mzML files. } \usage{ openMSfile(filename, backend = NULL, verbose = FALSE) @@ -13,12 +13,12 @@ isInitialized(object) fileName(object, ...) - + openIDfile(filename, verbose = FALSE) } \arguments{ \item{filename}{ - Path name of the netCDF, mzData, mzXML or mzML file to + Path name of the netCDF, mzXML or mzML file to read/write. } \item{backend}{ @@ -38,7 +38,7 @@ \code{mzR} object, open 'filename' file and all header information is loaded as a Rcpp module and made accessible through the \code{pwiz} slot of the resulting object. - + The \code{openIDfile} constructor will create a new format-specifc \code{mzR} object, open 'filename' file and all information is loaded as a Rcpp module. The mzid format is supported throught @@ -65,7 +65,7 @@ mz <- openMSfile(file, backend = "pwiz") mz } - + file <- system.file("mzid", "Tandem.mzid.gz", package="msdata") mzid <- openIDfile(file) softwareInfo(mzid) diff --git a/src/RcppIdentModule.cpp b/src/RcppIdentModule.cpp index 1cf49b132..9adf11aa0 100644 --- a/src/RcppIdentModule.cpp +++ b/src/RcppIdentModule.cpp @@ -9,7 +9,7 @@ RCPP_MODULE(Ident) class_( "Ident" ) .constructor("Initialises a new Rccp ident object.") - .method( "open", &RcppIdent::open, "Opens a mass spec file (mzXML, mzData, etc.) and creates a pwiz object" ) + .method( "open", &RcppIdent::open, "Opens a mass spec file (mzXML, mzML, etc.) and creates a pwiz object" ) .method( "getIDInfo", &RcppIdent::getIDInfo, "Basic information about this mzid files" ) .method( "getPsmInfo", &RcppIdent::getPsmInfo, "Basic information about this mzid files" ) .method( "getModInfo", &RcppIdent::getModInfo, "Modification information about this mzid files" ) diff --git a/src/RcppPwizModule.cpp b/src/RcppPwizModule.cpp index b5c3f1685..599a33514 100644 --- a/src/RcppPwizModule.cpp +++ b/src/RcppPwizModule.cpp @@ -9,9 +9,9 @@ RCPP_MODULE(Pwiz) class_( "Pwiz" ) .constructor("Initialises a new Rccp pwiz object.") - .method( "open", &RcppPwiz::open, "Opens a mass spec file (mzXML, mzData, etc.) and creates a pwiz object" ) - .method( "close", &RcppPwiz::close, "Close the connection to a mass spec file (mzXML, mzData, etc.)." ) - // .method( "writeMSfile", &RcppPwiz::writeMSfile, "Write a pwiz object into files (mzXML, mzData, etc.)" ) + .method( "open", &RcppPwiz::open, "Opens a mass spec file (mzXML, mzML, etc.) and creates a pwiz object" ) + .method( "close", &RcppPwiz::close, "Close the connection to a mass spec file (mzXML, mzML, etc.)." ) + // .method( "writeMSfile", &RcppPwiz::writeMSfile, "Write a pwiz object into files (mzXML, etc.)" ) .method( "writeSpectrumList", &RcppPwiz::writeSpectrumList, "Write the spectrum list to an mzML file." ) .method( "copyWriteMSfile", &RcppPwiz::copyWriteMSfile, "Copy general content from the originalting MS file, add the provided spectrum list and write the data to a new mzML file." ) .method( "getFilename", &RcppPwiz::getFilename, "Returns the mass spec filename.") diff --git a/vignettes/mzR.Rmd b/vignettes/mzR.Rmd index dbc230764..9f900ba24 100644 --- a/vignettes/mzR.Rmd +++ b/vignettes/mzR.Rmd @@ -13,22 +13,23 @@ bibliography: mzR.bib vignette: > %\VignetteEngine{knitr::rmarkdown} %\VignetteIndexEntry{Accessin raw mass spectrometry and identification data} - %\VignetteKeywords{mzXML, mzData, netCDF, mzML, mzIdentML, mass spectrometry, proteomics, metabolomics} + %\VignetteKeywords{mzXML, netCDF, mzML, mzIdentML, mass spectrometry, proteomics, metabolomics} %\VignetteEncoding{UTF-8} %\VignettePackage{mzR} --- # Introduction -The `r BiocStyle::Biocpkg("mzR")` package aims at providing a common, low-level -interface to several mass spectrometry data formats, namely `mzData` -[@Orchard2007], `mzXML` [@Pedrioli2004], `mzML` [@Martens2010] for raw -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 -`r BiocStyle::Biocpkg("MSnbase")` [@Gatto:2012]. These packages also provide more -convenient, high-level interfaces to raw and identification. data +The `r BiocStyle::Biocpkg("mzR")` package aims at providing a common, +low-level interface to several mass spectrometry data formats, namely, +`mzXML` [@Pedrioli2004], `mzML` [@Martens2010] for raw 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 `r +BiocStyle::Biocpkg("MSnbase")` [@Gatto:2012]. These packages also +provide more convenient, high-level interfaces to raw and +identification. data Most importantly, access to the data should be fast and memory efficient. This is made possible by allowing on-disk random file @@ -110,7 +111,7 @@ depends on the MS software which converted the data. # Example -## `mzXML`/`mzML`/`mzData` files +## `mzXML`/`mzML` files A short example sequence to read data from a mass spectrometer. First open the file.