diff -Nru r-cran-readbrukerflexdata-1.6.3/DESCRIPTION r-cran-readbrukerflexdata-1.7/DESCRIPTION --- r-cran-readbrukerflexdata-1.6.3/DESCRIPTION 2013-04-28 13:08:19.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/DESCRIPTION 2013-08-10 16:13:34.000000000 +0000 @@ -1,13 +1,13 @@ Package: readBrukerFlexData -Version: 1.6.3 -Date: 2013-04-28 +Version: 1.7 +Date: 2013-08-10 Title: Reads mass spectrometry data in Bruker *flex format Authors@R: person("Sebastian", "Gibb", role=c("aut", "cre"), - email="mail@sebastiangibb.de") -Depends: R (>= 2.14.0) + email="mail@sebastiangibb.de") +Depends: R (>= 2.15.0) Suggests: MALDIquant (>= 1.0) -Description: Reads data files acquired by MALDI-TOF MS on Bruker - Daltonics machines of the *flex series. +Description: Reads data files acquired by MALDI-TOF MS on Bruker Daltonics + machines of the *flex series. License: GPL (>= 3) URL: http://strimmerlab.org/software/maldiquant/ https://github.com/sgibb/readBrukerFlexData/ @@ -19,9 +19,9 @@ 'readAcquFile-functions.R' 'readBrukerFlexDir-functions.R' 'readBrukerFlexFile-functions.R' 'readFidFile-functions.R' 'sampleName-functions.R' 'tof2mass-functions.R' -Packaged: 2013-04-28 10:04:55 UTC; sebastian +Packaged: 2013-08-10 15:32:47 UTC; sebastian Author: Sebastian Gibb [aut, cre] Maintainer: Sebastian Gibb NeedsCompilation: no Repository: CRAN -Date/Publication: 2013-04-28 15:08:19 +Date/Publication: 2013-08-10 18:13:34 diff -Nru r-cran-readbrukerflexdata-1.6.3/MD5 r-cran-readbrukerflexdata-1.7/MD5 --- r-cran-readbrukerflexdata-1.6.3/MD5 2013-04-28 13:08:19.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/MD5 2013-08-10 16:13:34.000000000 +0000 @@ -1,16 +1,16 @@ -02f46a2ba3c4f2d50e0b890d57f10155 *DESCRIPTION +a340ac75edd8404c1adc8f6f876de0e9 *DESCRIPTION 65fc6706cbe7df7357e5263263819dd9 *NAMESPACE -07bb64ee3099b985bd79c2cb93ba3604 *NEWS +b120a03e87a82aec0815f5d1d156fcf2 *NEWS 3af5176f5a2d53bd7e33999b75483b94 *R/cpSpecHpcMzXml-data.R 45f6ac1c7e92d8d7389aada0cabcb582 *R/double2singlePrecision-functions.R 508a7700b53501ac07707350afec7298 *R/grepAcquValue-functions.R -163b36e97a59fa8b76d8af3d9a816046 *R/hpc-functions.R +7a028b16b4c9d2eb1efdbd3cdd8c9a5d *R/hpc-functions.R ebf4bdc6b0dd815233cffb4649134f20 *R/mqReadBrukerFlex-functions.R -b0398fcdd9349c124e0fcc85474417b4 *R/package.R +80bdec5f1b625cd47d214ad065be0849 *R/package.R cd2df5624232c12162bacfe63ddfa48d *R/readAcquFile-functions.R -18ca2f6efe4e9da078c64be2603eb502 *R/readBrukerFlexDir-functions.R -8f294f381169781825a528fe24ff5b4e *R/readBrukerFlexFile-functions.R -ff2f7beb66e03dd18493cef44f4def87 *R/readFidFile-functions.R +6fb3f82700f6272d5d80bfa00ae6a746 *R/readBrukerFlexDir-functions.R +9e8659313b36b1f427e87f43c28112ac *R/readBrukerFlexFile-functions.R +7ccbabd8c7a3c3f08a80cac327129059 *R/readFidFile-functions.R d8fa78c093f236be8084b9edf2022059 *R/sampleName-functions.R 61f4159d7a248e9d6901bd2781c01fe5 *R/tof2mass-functions.R 0a984d7b36f80792aaf6170017d7655b *data/cpSpecHpcMzXml.RData @@ -30,9 +30,9 @@ cf45f46aae2d99c71b792d6fb1e8b515 *man/hpc.Rd a4226c7349413ff3894a5c0bd81b7104 *man/mqReadBrukerFlex.Rd 9a4819360982becb78a60c94c60cfcf7 *man/readAcquFile.Rd -d100d8a65316e146e078356db97178c1 *man/readBrukerFlexData-package.Rd +d9400fe0c6e9b9de9d0ab9435ca9d837 *man/readBrukerFlexData-package.Rd 8fecadc9c3d34b6fbb4b2922d3351429 *man/readBrukerFlexDir.Rd -dafdc373b8b3d97170f340f3c3aec676 *man/readBrukerFlexFile.Rd +1696103d1810cf8b5498e89335d5087e *man/readBrukerFlexFile.Rd ff781b8dd8d027cabae93d761b590fb3 *man/readFidFile.Rd 64da82352560ee477c9989200bfe8e43 *man/sampleName.Rd 99aa9d59f5e132be5bdc01a109060749 *man/tof2mass.Rd diff -Nru r-cran-readbrukerflexdata-1.6.3/NEWS r-cran-readbrukerflexdata-1.7/NEWS --- r-cran-readbrukerflexdata-1.6.3/NEWS 2013-04-28 10:04:19.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/NEWS 2013-08-10 13:56:31.000000000 +0000 @@ -1,6 +1,14 @@ RELEASE HISTORY OF THE "readBrukerFlexData" PACKAGE =================================================== +Version 1.7 [2013-08-10]: +- Always return intensity values as "double". +- Now all negative intensity values are replaced by zero. + This could be disabled by setting the new argument + "keepNegativeIntensities" to "TRUE" [not recommended]. +- Replace all paste(..., sep="") by paste0; + now readBrukerFlexData depends on R >= 2.15. + Version 1.6.3 [2013-04-28]: - Fetch spectrum position from IMS data files. diff -Nru r-cran-readbrukerflexdata-1.6.3/R/hpc-functions.R r-cran-readbrukerflexdata-1.7/R/hpc-functions.R --- r-cran-readbrukerflexdata-1.6.3/R/hpc-functions.R 2013-03-28 06:54:17.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/R/hpc-functions.R 2013-06-02 10:52:19.000000000 +0000 @@ -189,7 +189,8 @@ ## before: reduce calculation time ## after: produce better results ## I also don't know whether to use >= or > (<=, <). - m <- mass[mass >= minMass & mass <= maxMass] + hpcRange <- mass >= minMass & mass <= maxMass + m <- mass[hpcRange] ## correction=c[0] + c[1]*cal_mass^1 + ... + c[n]*cal_mass^n ## mass=cal_mass - correction @@ -198,7 +199,7 @@ return(x - sum(hpcCoefficients * x^(0:l))) }) - mass[mass >= minMass & mass <= maxMass] <- m + mass[hpcRange] <- m return(mass) } diff -Nru r-cran-readbrukerflexdata-1.6.3/R/package.R r-cran-readbrukerflexdata-1.7/R/package.R --- r-cran-readbrukerflexdata-1.6.3/R/package.R 2013-04-28 10:04:12.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/R/package.R 2013-08-10 11:41:01.000000000 +0000 @@ -30,9 +30,9 @@ #' #' Package: \tab readBrukerFlexData \cr #' -#' Version: \tab 1.6.3\cr +#' Version: \tab 1.7\cr #' -#' Date: \tab 2013-04-28\cr +#' Date: \tab 2013-08-10\cr #' #' License: \tab GPL (>= 3)\cr #' diff -Nru r-cran-readbrukerflexdata-1.6.3/R/readBrukerFlexDir-functions.R r-cran-readbrukerflexdata-1.7/R/readBrukerFlexDir-functions.R --- r-cran-readbrukerflexdata-1.6.3/R/readBrukerFlexDir-functions.R 2012-12-13 15:34:17.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/R/readBrukerFlexDir-functions.R 2013-05-02 16:38:58.000000000 +0000 @@ -18,25 +18,25 @@ #' Reads recursively mass spectrometry data in Bruker Daltonics XMASS format. #' -#' This function leads recursively all mass spectrometry data in +#' This function leads recursively all mass spectrometry data in #' Bruker Daltonics XMASS format in a specified directory. #' #' @details #' See \code{\link[readBrukerFlexData]{readBrukerFlexFile}}. #' -#' @param brukerFlexDir \code{character}, path to \emph{directory} which +#' @param brukerFlexDir \code{character}, path to \emph{directory} which #' should be read recursively. #' @param removeCalibrationScans \code{logical}, if \code{TRUE} all scans in #' directories called \code{[Cc]alibration} will be ignored. #' @param removeMetaData \code{logical}, to calculate mass data a lot of #' meta data are needed. To save memory they could be deleted after -#' calculation. +#' calculation. #' @param useHpc \code{logical}, should Bruker Daltonics' High Precision -#' Calibration be used if available? (see also: +#' Calibration be used if available? (see also: #' \code{\link[readBrukerFlexData]{.hpc}}) #' @param useSpectraNames \code{logical}, if \code{TRUE} all list elements #' get an unique name from metaData otherwise file path is used. -#' (If \sQuote{removeMetaData} is \code{TRUE} \sQuote{useSpectraNames} +#' (If \sQuote{removeMetaData} is \code{TRUE} \sQuote{useSpectraNames} #' has no effect.) #' @param filterZeroIntensities \code{logical}, don't change it. If \code{TRUE} #' all intensities equal \code{0.0} are removed. @@ -60,17 +60,17 @@ #' @examples #' ## load library #' library("readBrukerFlexData") -#' +#' #' ## get examples directory #' exampleDirectory <- system.file("Examples", package="readBrukerFlexData") -#' +#' #' ## read example spectra #' spec <- readBrukerFlexDir(file.path(exampleDirectory, #' "2010_05_19_Gibb_C8_A1")) -#' +#' #' ## plot spectra #' plot(spec[[1]]$spectrum$mass, spec[[1]]$spectrum$intensity, type="n") -#' +#' #' l <- length(spec) #' legendStr <- character(l) #' for (i in seq(along=spec)) { @@ -78,26 +78,26 @@ #' col=rainbow(l)[i]) #' legendStr[i] <- spec[[i]]$metaData$fullName #' } -#' +#' #' ## draw legend #' legend(x="topright", legend=legendStr, col=rainbow(l), lwd=1) #' -readBrukerFlexDir <- function(brukerFlexDir, removeCalibrationScans=TRUE, - removeMetaData=FALSE, useHpc=TRUE, - useSpectraNames=TRUE, +readBrukerFlexDir <- function(brukerFlexDir, removeCalibrationScans=TRUE, + removeMetaData=FALSE, useHpc=TRUE, + useSpectraNames=TRUE, filterZeroIntensities=FALSE, verbose=FALSE) { if (verbose) { message("Look for spectra in ", sQuote(brukerFlexDir), " ...") } - + if ((!file.exists(brukerFlexDir)) || (!file.info(brukerFlexDir)$isdir)) { stop("Directory ", sQuote(brukerFlexDir), " doesn't exists or is no directory!") } - + ## look for fid files (alphabetical sort) files <- list.files(path=brukerFlexDir, pattern="^fid$", recursive=TRUE) - + ## remove calibrations scans? if (removeCalibrationScans) { calibrationScans <- grep(pattern="[Cc]alibration", x=files, value=TRUE) @@ -105,17 +105,17 @@ files <- setdiff(files, calibrationScans) } } - + if (length(files) <= 0) { stop("Directory doesn't contain any fid file.") } - + ## generate 'path/files' files <- sapply(files, function(x) { x <- file.path(brukerFlexDir, x) return(x) }) - + ## read fid files brukerFlexData <- lapply(X=files, FUN=function(f) { return(readBrukerFlexFile(fidFile=f, removeMetaData=removeMetaData, @@ -123,24 +123,24 @@ filterZeroIntensities=filterZeroIntensities, verbose=verbose)) }) - + if (!removeMetaData & useSpectraNames) { ## rewrite names if metadata exists if (verbose) { message("look for spectra names ...") } - + names(brukerFlexData) <- sapply(X=brukerFlexData, FUN=function(x) { if (!is.null(x$metaData$sampleName)) { if (!is.na(x$metaData$sampleName)) { - return(paste("s", x$metaData$fullName, ".", - x$metaData$targetIdString, sep="")) + return(paste0("s", x$metaData$fullName, ".", + x$metaData$targetIdString)) } } return(NA) }, USE.NAMES=FALSE) } - + return(brukerFlexData) } - + diff -Nru r-cran-readbrukerflexdata-1.6.3/R/readBrukerFlexFile-functions.R r-cran-readbrukerflexdata-1.7/R/readBrukerFlexFile-functions.R --- r-cran-readbrukerflexdata-1.6.3/R/readBrukerFlexFile-functions.R 2013-02-14 22:47:11.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/R/readBrukerFlexFile-functions.R 2013-08-10 15:29:38.000000000 +0000 @@ -1,4 +1,4 @@ -## Copyright 2010-2012 Sebastian Gibb +## Copyright 2010-2013 Sebastian Gibb ## ## ## This file is part of readBrukerFlexData for R and related languages. @@ -118,6 +118,12 @@ #' CompassXport 3.0.3 will filter out zero (0.0) intensities #' when exporting to mzXML or mzData \ldots} #' +#' \code{keepNegativeIntensities}: Change default value is +#' \bold{not recommended}! If \code{TRUE} negative intensity values are not +#' replaced by zero. This parameter exists only to be compatible to +#' Bruker Daltonics CompassXport. +#' +#' #' @param fidFile \code{character}, path to \emph{fid} file which should be #' read. #' @param removeMetaData, \code{logical}, to calculate mass data a lot of meta @@ -128,6 +134,10 @@ #' @param filterZeroIntensities \code{logical}, don't change it. #' If \code{TRUE} all intensities equal \code{0.0} are removed. #' (see also: \sQuote{Details} section) +#' @param keepNegativeIntensities \code{logical}, don't change it. +#' If \code{FALSE} all intensities less than zero are replaced by +#' zero. +#' (see also: \sQuote{Details} section) #' @param verbose \code{logical}, print verbose messages? #' #' @return @@ -141,6 +151,7 @@ #' } #' @export #' @seealso +#' \url{https://github.com/sgibb/readBrukerFlexData/wiki}, #' \code{\link[readBrukerFlexData]{readBrukerFlexDir}}, #' \code{\link[readBrukerFlexData]{.hpc}} #' @keywords IO @@ -163,7 +174,9 @@ #' plot(spec$spectrum$mass, spec$spectrum$intensity, type="l", col="red") #' readBrukerFlexFile <- function(fidFile, removeMetaData=FALSE, useHpc=TRUE, - filterZeroIntensities=FALSE, verbose=FALSE) { + filterZeroIntensities=FALSE, + keepNegativeIntensities=FALSE, + verbose=FALSE) { if (verbose) { message("Reading spectrum from ", sQuote(fidFile), " ...") } @@ -189,6 +202,12 @@ tof <- as.double(metaData$timeDelay + ((0:(metaData$number-1)) * metaData$timeDelta)) + ## replace negative intensity values by zero + isNegative <- which(intensity < 0) + if (!keepNegativeIntensities && length(isNegative)) { + intensity[isNegative] <- 0 + } + ## remove times which have no intensity (intensity == 0), e.g. generated by ## REFLECTOR mode ## for details see "Release Notes for CompassXport 3.0.3" @@ -198,7 +217,7 @@ ## CompassXport 3.0.3 will filter out zero (0.0) intensities ## when exporting to mzXML or mzData ..." if (filterZeroIntensities) { - notNull <- intensity > 0 + notNull <- which(intensity > 0) intensity <- intensity[notNull] tof <- tof[notNull] } diff -Nru r-cran-readbrukerflexdata-1.6.3/R/readFidFile-functions.R r-cran-readbrukerflexdata-1.7/R/readFidFile-functions.R --- r-cran-readbrukerflexdata-1.6.3/R/readFidFile-functions.R 2012-09-10 16:58:47.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/R/readFidFile-functions.R 2013-08-09 14:21:37.000000000 +0000 @@ -24,12 +24,12 @@ #' #' @param fidFile \code{character} path to fid file e.g. #' Pankreas_HB_L_061019_A10/0_a19/1/1SLin/fid -#' @param nIntensities number of data entries -#' (total count; get from acqu file) +#' @param nIntensities number of data entries +#' (total count; get from acqu file) #' @param endian endianness of the fid file #' (\sQuote{little} or \sQuote{big}; default: \sQuote{little}) -#' -#' @return +#' +#' @return #' A vector of intensity values. #' @seealso #' \code{\link[readBrukerFlexData]{.readAcquFile}}, @@ -41,11 +41,11 @@ if (!file.exists(fidFile)) { stop("File ", sQuote(fidFile), " doesn't exists!") } - + con <- file(fidFile, "rb") intensity <- readBin(con, integer(), n=nIntensities, size=4, endian=endian) close(con) - - return(intensity) + + return(as.double(intensity)) } - + diff -Nru r-cran-readbrukerflexdata-1.6.3/debian/changelog r-cran-readbrukerflexdata-1.7/debian/changelog --- r-cran-readbrukerflexdata-1.6.3/debian/changelog 2013-04-28 19:13:36.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/debian/changelog 2013-08-28 11:43:22.000000000 +0000 @@ -1,6 +1,16 @@ -r-cran-readbrukerflexdata (1.6.3-1) unstable; urgency=low +r-cran-readbrukerflexdata (1.7-1) unstable; urgency=low * New upstream release. + * debian/control.in: + - use canonical URI in Vcs-Git/Vcs-Browser. + - set debhelper (>= 9) + * Uploaded by Filippo Rusconi . + + -- The Debichem Group Wed, 28 Aug 2013 13:42:19 +0200 + +r-cran-readbrukerflexdata (1.6.3-1) unstable; urgency=low + + * New upstream release. Upload by Filippo Rusconi . -- The Debichem Group Sun, 28 Apr 2013 21:12:31 +0200 diff -Nru r-cran-readbrukerflexdata-1.6.3/debian/control r-cran-readbrukerflexdata-1.7/debian/control --- r-cran-readbrukerflexdata-1.6.3/debian/control 2013-05-28 10:42:04.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/debian/control 2013-08-28 11:44:11.000000000 +0000 @@ -3,11 +3,11 @@ Priority: optional Maintainer: The Debichem Group Uploaders: Filippo Rusconi -Build-Depends: debhelper (>= 8), r-base-dev (>= 2.14.0) +Build-Depends: debhelper (>= 9), r-base-dev (>= 2.15.0) Standards-Version: 3.9.4 Homepage: http://cran.r-project.org/web/packages/readBrukerFlexData/index.html -Vcs-Git: git://git.debian.org/git/debichem/packages/r-cran-readbrukerflexdata.git -Vcs-Browser: http://git.debian.org/?p=debichem/packages/r-cran-readbrukerflexdata.git +Vcs-Git: git://anonscm.debian.org/debichem/packages/r-cran-readbrukerflexdata.git +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debichem/packages/r-cran-readbrukerflexdata.git Package: r-cran-readbrukerflexdata Architecture: any diff -Nru r-cran-readbrukerflexdata-1.6.3/debian/control.in r-cran-readbrukerflexdata-1.7/debian/control.in --- r-cran-readbrukerflexdata-1.6.3/debian/control.in 2013-04-28 19:13:36.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/debian/control.in 2013-08-28 11:43:22.000000000 +0000 @@ -3,11 +3,11 @@ Priority: optional Maintainer: The Debichem Group Uploaders: Filippo Rusconi -Build-Depends: debhelper (>= 8), r-base-dev (@R_DEPENDS_VERSION@) +Build-Depends: debhelper (>= 9), r-base-dev (@R_DEPENDS_VERSION@) Standards-Version: 3.9.4 Homepage: http://cran.r-project.org/web/packages/readBrukerFlexData/index.html -Vcs-Git: git://git.debian.org/git/debichem/packages/r-cran-readbrukerflexdata.git -Vcs-Browser: http://git.debian.org/?p=debichem/packages/r-cran-readbrukerflexdata.git +Vcs-Git: git://anonscm.debian.org/debichem/packages/r-cran-readbrukerflexdata.git +Vcs-Browser: http://anonscm.debian.org/gitweb/?p=debichem/packages/r-cran-readbrukerflexdata.git Package: r-cran-readbrukerflexdata Architecture: any diff -Nru r-cran-readbrukerflexdata-1.6.3/man/readBrukerFlexData-package.Rd r-cran-readbrukerflexdata-1.7/man/readBrukerFlexData-package.Rd --- r-cran-readbrukerflexdata-1.6.3/man/readBrukerFlexData-package.Rd 2013-04-28 10:04:55.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/man/readBrukerFlexData-package.Rd 2013-08-10 11:42:47.000000000 +0000 @@ -15,9 +15,9 @@ Package: \tab readBrukerFlexData \cr - Version: \tab 1.6.3\cr + Version: \tab 1.7\cr - Date: \tab 2013-04-28\cr + Date: \tab 2013-08-10\cr License: \tab GPL (>= 3)\cr diff -Nru r-cran-readbrukerflexdata-1.6.3/man/readBrukerFlexFile.Rd r-cran-readbrukerflexdata-1.7/man/readBrukerFlexFile.Rd --- r-cran-readbrukerflexdata-1.6.3/man/readBrukerFlexFile.Rd 2012-12-13 15:34:17.000000000 +0000 +++ r-cran-readbrukerflexdata-1.7/man/readBrukerFlexFile.Rd 2013-08-10 15:29:44.000000000 +0000 @@ -4,7 +4,7 @@ \usage{ readBrukerFlexFile(fidFile, removeMetaData = FALSE, useHpc = TRUE, filterZeroIntensities = FALSE, - verbose = FALSE) + keepNegativeIntensities = FALSE, verbose = FALSE) } \arguments{ \item{fidFile}{\code{character}, path to \emph{fid} file @@ -22,6 +22,11 @@ it. If \code{TRUE} all intensities equal \code{0.0} are removed. (see also: \sQuote{Details} section)} + \item{keepNegativeIntensities}{\code{logical}, don't + change it. If \code{FALSE} all intensities less than + zero are replaced by zero. (see also: \sQuote{Details} + section)} + \item{verbose}{\code{logical}, print verbose messages?} } \value{ @@ -134,6 +139,11 @@ operation time and to keep export file sizes small, CompassXport 3.0.3 will filter out zero (0.0) intensities when exporting to mzXML or mzData \ldots} + + \code{keepNegativeIntensities}: Change default value is + \bold{not recommended}! If \code{TRUE} negative intensity + values are not replaced by zero. This parameter exists + only to be compatible to Bruker Daltonics CompassXport. } \examples{ ## load library @@ -153,6 +163,7 @@ plot(spec$spectrum$mass, spec$spectrum$intensity, type="l", col="red") } \seealso{ + \url{https://github.com/sgibb/readBrukerFlexData/wiki}, \code{\link[readBrukerFlexData]{readBrukerFlexDir}}, \code{\link[readBrukerFlexData]{.hpc}} }