R/readAcquFile-functions.R
In sgibb/readBrukerFlexData: Reads Mass Spectrometry Data in Bruker *flex Format
Defines functions
.readAcquFile
Documented in
.readAcquFile
## Copyright 2010-2014 Sebastian Gibb
## <mail@sebastiangibb.de>
##
## This file is part of readBrukerFlexData for R and related languages.
##
## readBrukerFlexData is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.
##
## readBrukerFlexData is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with readBrukerFlexData. If not, see <https://www.gnu.org/licenses/>
#' Reads an acqu file.
#'
#' This function reads constants, calibrations values and a lot of more from
#' \emph{acqu} files.
#'
#' @param fidFile \code{character}, path to corresponding fid file
#' (e.g. \code{Pankreas_HB_L_061019_A10/0_a19/1/1SLin/fid})
#' @param verbose \code{logical}, print verbose messages?
#'
#' @return
#' a \code{list} with metadata
#'
#' @seealso \code{\link[readBrukerFlexData]{readBrukerFlexFile}},
#' @rdname readAcquFile
#' @keywords internal IO
#'
## We have to import the following data to calculating mass:
## $BYTORDA: endianness, 0==little, 1==big
## => metaData$byteOrder
## $TD: total number of measured time periods
## => metaData$number
## $DELAY: first measured intensity after $DELAY ns
## => metaData$timeDelay
## $DW: ns between measured time periods
## => metaData$timeDelta
## $ML1: calibration constant
## => metaData$calibrationConstants[1]
## $ML2: calibration constant
## => metaData$calibrationConstants[2]
## $ML3: calibration constant
## => metaData$calibrationConstants[3]
##
## if we want to use High Precision Calibration (HPC), we need:
## $HPClBHi: upper mass threshold
## => metaData$hpcLimits["maxMass"]
## $HPClBLo: lower mass threshold
## => metaData$hpcLimits["minMass"]
## $HPClOrd: polynomial order
## => metaData$hpcOrder
## $HPClUse: maybe using of HPC? (seems always be "yes" in our test data)
## => metaData$hpcUse
## $HPCStr: polynomial coefficients in a string
## => metaData$hpcCoefficients
##
## we try to import [optional]:
## DATATYPE
## SPECTROMETER/DATASYSTEM
## => metaData$dataSystem
## .SPECTROMETER TYPE
## => metaData$spectrometerType
## .INLET
## => metaData$inlet
## .IONIZATION MODE
## => metaData$ionizationMode
## $DATE
## => metaData$date
## $ACQMETH
## => metaData$acquisitionMethod
## $AQ_DATE
## => metaData$acquisitionDate
## $AQ_mod
## => metaData$acquisitionMode
## $AQOP_mod
## => metaData$acquisitionOperatorMode
## => metaData$tofMode (replaces file path based method)
## $ATTEN
## => metaData$laserAttenuation
## $COM[1:4]
## => metaData$comments
## $DEFLON
## => metaData$deflection
## $DIGTYP
## => metaData$digitizerType
## $DPCAL1
## => metaData$deflectionPulserCal1
## $DPMASS
## => metaData$deflectionPulserMass
## $FCVer
## => metaData$flexControlVersion
## $ID_raw
## => metaData$id
## $INSTRUM
## => metaData$instrument
## $InstrID
## => metaData$instrumentId
## $InstrTyp
## => metaData$instrumentType
## $Masserr
## => metaData$massError
## $NoSHOTS: number of laser shots
## => metaData$laserShots
## $SPType
## => metaData$spectrumType
## $PATCHNO: sample position on target
## => metaData$patch
## $PATH: original file path (on Bruker flex series controller PC)
## => metaData$path
## $REPHZ
## => metaData$laserRepetition
## $SPOTNO: same as $PATCHNO (in older files often empty, that's why we use
## $PATCHNO instead)
## => metaData$spot
## $TgIDS: target ids
## => metaData$targetIdString
## $TgCount: number of measurement with this target
## => metaData$targetCount
## $TgSer: target serial number
## => metaData$targetSerialNumber
## $TgTyp: target type number
## => metaData$targetTypeNumber
##
## import from file path:
## full current path to fid file:
## => metaData$fidFile
## sample name
## => metaData$sampleName
##
.readAcquFile <- function(fidFile, verbose=FALSE) {
acquFile <- sub(pattern="fid$", x=fidFile, replacement="acqu")
acquFiles <- c(acquFile, paste0(acquFile, "s"))
acquFile <- acquFiles[which.max(file.exists(acquFiles))]
if (!file.exists(acquFile)) {
stop("File ", sQuote(acquFile), " doesn't exists!")
}
if (verbose) {
message("Reading metadata from ", sQuote(acquFile), " ...")
}
con <- file(acquFile, "rt")
acquLines <- readLines(con, n=-1)
close(con)
## collect data
metaData <- list()
## endianness
isBigEndian <- as.integer(.grepAcquValue("##\\$BYTORDA=", acquLines)) == 1L
metaData$byteOrder <- ifelse(isBigEndian, "big", "little")
## obligate
metaData$number <- as.double(.grepAcquValue("##\\$TD=", acquLines))
metaData$timeDelay <- .grepAcquDoubleValue("##\\$DELAY=", acquLines)
metaData$timeDelta <- .grepAcquDoubleValue("##\\$DW=", acquLines)
metaData$calibrationConstants <-
c(c1=.grepAcquDoubleValue("##\\$ML1=", acquLines),
c2=.grepAcquDoubleValue("##\\$ML2=", acquLines),
c3=.grepAcquDoubleValue("##\\$ML3=", acquLines))
## obligate HPC
metaData$hpcLimits <-
c(minMass=.grepAcquDoubleValue("##\\$HPClBLo=", acquLines),
maxMass=.grepAcquDoubleValue("##\\$HPClBHi=", acquLines))
metaData$hpcOrder <- as.double(.grepAcquValue("##\\$HPClOrd=", acquLines))
metaData$hpcUse <-
as.logical(.grepAcquValue("##\\$HPClUse=", acquLines) == "yes")
## was HPC involved? metaData$hpcUse seems to be always true
isHPCused <- isTRUE(metaData$hpcUse &&
metaData$hpcLimits["maxMass"] > 0L &&
metaData$hpcLimits["minMass"] > 0L &&
metaData$hpcOrder > 0L)
if (isHPCused) {
hpcStr <- .grepAcquValue("##\\$HPCStr=", acquLines)
hpcConstants <- .extractHPCConstants(hpcStr)
metaData$hpcCoefficients <- hpcConstants$coefficients
metaData$hpcCalibrationConstant0 <- hpcConstants$calibrationConstant0
metaData$hpcCalibrationConstant2 <- hpcConstants$calibrationConstant2
}
# https://github.com/sgibb/MALDIquantForeign/issues/19
# https://github.com/sgibb/readBrukerFlexData/issues/3
metaData$v1tofCalibration <-
grepl("V1.0CTOF2CalibrationConstants",
.grepAcquValue("##\\$NTBCal=", acquLines))
metaData$v1tofCalibrationConstants <-
.extractV10CTOF2CalibrationConstants(
.grepAcquValue("##\\$NTBCal=", acquLines)
)
## obligate LIFT
metaData$lift <- c(.grepAcquDoubleValue("##\\$Lift1=", acquLines),
.grepAcquDoubleValue("##\\$Lift2=", acquLines))
metaData$tlift <- .grepAcquDoubleValue("##\\$TLift=", acquLines)
## optional
metaData$dataType <- .grepAcquValue("##DATATYPE=", acquLines)
metaData$dataSystem <- .grepAcquValue("##SPECTROMETER/DATASYSTEM=", acquLines)
metaData$spectrometerType <-
.grepAcquValue("##.SPECTROMETER TYPE=", acquLines)
metaData$inlet <- .grepAcquValue("##.INLET=", acquLines)
metaData$ionizationMode <- .grepAcquValue("##.IONIZATION MODE=", acquLines)
metaData$date <- .grepAcquValue("##\\$DATE=", acquLines)
metaData$acquisitionMethod <- .grepAcquValue("##\\$ACQMETH=", acquLines)
metaData$acquisitionDate <- .grepAcquValue("##\\$AQ_DATE=", acquLines)
aq_mod <- .grepAcquValue("##\\$AQ_mod=", acquLines)
if (length(aq_mod)) {
metaData$acquisitionMode <- switch(aq_mod,
"0" = { "qf" },
"1" = { "qsim" },
"2" = { "qseq" },
{ aq_mod }
)
}
aqop <- .grepAcquValue("##\\$AQOP_m=", acquLines)
if (length(aqop)) {
metaData$tofMode <- switch(aqop,
"0" = { "LINEAR" },
"1" = { "REFLECTOR" },
{ aqop }
)
}
metaData$acquisitionOperatorMode <- metaData$tofMode
metaData$laserAttenuation <- .grepAcquDoubleValue("##\\$ATTEN=", acquLines)
metaData$comments <- .grepAcquValue("##\\$CMT.*=", acquLines)
metaData$deflection <-
as.logical(.grepAcquValue("##\\$DEFLON=", acquLines) == "yes")
digtyp <- .grepAcquValue("##\\$DIGTYP=", acquLines)
if (length(digtyp)) {
metaData$digitizerType <- switch(digtyp,
"0" = { "unknown" },
"1" = { "Lecroy LSA1000" },
"2" = { "Acqiris DP105" },
"3" = { "Acqiris DP110" },
"4" = { "Acqiris DP211" },
"5" = { "Acqiris DP240" },
"6" = { "Acqiris AP200" },
"7" = { "Acqiris AP240" },
"8" = { "Acqiris DC440" },
"9" = { "Acqiris DC282" },
"10" = { "Acqiris Unknown subtype" },
"11" = { "Gage" },
"12" = { "Simulator" },
"13" = { "Lecroy WaveRunner" },
"14" = { "Acqiris U1084A" },
"15" = { "NI 5154" },
"16" = { "LeCroy LSA2000" },
"17" = { "Acqiris DP1400" },
"18" = { "NI 5155" },
"19" = { "Bruker BD0G5" },
{ digtyp }
)
}
metaData$deflectionPulserCal1 <-
.grepAcquDoubleValue("##\\$DPCAL1=", acquLines)
metaData$deflectionPulserMass <-
.grepAcquDoubleValue("##\\$DPMASS=", acquLines)
metaData$flexControlVersion <- .grepAcquValue("##\\$FCVer=", acquLines)
metaData$id <- .grepAcquValue("##\\$ID_raw=", acquLines)
metaData$instrument <- .grepAcquValue("##\\$INSTRUM=", acquLines)
metaData$instrumentId <- .grepAcquValue("##\\$InstrID=", acquLines)
instrumentType <- .grepAcquValue("##\\$InstTyp=", acquLines)
if (length(instrumentType)) {
metaData$instrumentType <- switch(instrumentType,
"0" = { "autoflex" },
"1" = { "ultraflex" },
"2" = { "ultraflexTOF/TOF" },
"3" = { "reflex" },
"4" = { "biflex" },
"5" = { "omniflex" },
"6" = { "genoflex" },
"7" = { "massarray" },
"8" = { "autoflexTOF/TOF" },
"9" = { "microflex" },
"10" = { "MT10" },
{ instrumentType }
)
}
metaData$massError <- .grepAcquDoubleValue("##\\$Masserr=", acquLines)
metaData$laserShots <- as.double(.grepAcquValue("##\\$NoSHOTS=", acquLines))
if (metaData$laserShots == 0L) {
warning("File ", sQuote(fidFile), " seems to be empty because ",
"no laser shots applied to this sample.")
}
metaData$patch <- .grepAcquValue("##\\$PATCHNO=", acquLines)
## imaging data
if (length(metaData$patch) &&
grepl(pattern="(R[0-9]+)?X[0-9]+Y[0-9]+", x=metaData$patch,
ignore.case=TRUE)) {
rx <- gregexpr(pattern="[XY][0-9]+", text=metaData$patch)[[1L]]
pos <- substring(metaData$patch, rx+1L, rx+attr(rx, "match.length")-1L)
if (length(pos) == 2L) {
pos <- as.double(pos)
metaData$imaging <- list(pos=c(x=pos[1L], y=pos[2L]))
}
}
metaData$path <- .grepAcquValue("##\\$PATH=", acquLines)
metaData$laserRepetition <- .grepAcquDoubleValue("##\\$REPHZ=", acquLines)
metaData$spot <- .grepAcquValue("##\\$SPOTNO=", acquLines)
sptype <- .grepAcquValue("##\\$SPType=", acquLines)
if (length(sptype)) {
metaData$spectrumType <- switch(sptype,
"0" = { "TOF" },
"1" = { "PSD" },
"2" = { "LIFT" },
"3" = { "PSDSegment" },
{ sptype }
)
}
metaData$targetCount <- as.double(.grepAcquValue("##\\$TgCount", acquLines))
metaData$targetIdString <- .grepAcquValue("##\\$TgIDS", acquLines)
metaData$targetSerialNumber <- .grepAcquValue("##\\$TgSer", acquLines)
metaData$targetTypeNumber <- .grepAcquValue("##\\$TgTyp", acquLines)
metaData$file <- fidFile
metaData$sampleName <- .sampleName(fidFile)
metaData$fullName <- paste(metaData$sampleName, metaData$patch, sep=".")
metaData$name <- metaData$fullName
metaData
}
sgibb/readBrukerFlexData documentation built on Jan. 26, 2024, 10:08 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions .readAcquFile
Documented in .readAcquFile
## Copyright 2010-2014 Sebastian Gibb
## <mail@sebastiangibb.de>
##
## This file is part of readBrukerFlexData for R and related languages.
##
## readBrukerFlexData is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later version.
##
## readBrukerFlexData is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public License
## along with readBrukerFlexData. If not, see <https://www.gnu.org/licenses/>
#' Reads an acqu file.
#'
#' This function reads constants, calibrations values and a lot of more from
#' \emph{acqu} files.
#'
#' @param fidFile \code{character}, path to corresponding fid file
#' (e.g. \code{Pankreas_HB_L_061019_A10/0_a19/1/1SLin/fid})
#' @param verbose \code{logical}, print verbose messages?
#'
#' @return
#' a \code{list} with metadata
#'
#' @seealso \code{\link[readBrukerFlexData]{readBrukerFlexFile}},
#' @rdname readAcquFile
#' @keywords internal IO
#'
## We have to import the following data to calculating mass:
## $BYTORDA: endianness, 0==little, 1==big
## => metaData$byteOrder
## $TD: total number of measured time periods
## => metaData$number
## $DELAY: first measured intensity after $DELAY ns
## => metaData$timeDelay
## $DW: ns between measured time periods
## => metaData$timeDelta
## $ML1: calibration constant
## => metaData$calibrationConstants[1]
## $ML2: calibration constant
## => metaData$calibrationConstants[2]
## $ML3: calibration constant
## => metaData$calibrationConstants[3]
##
## if we want to use High Precision Calibration (HPC), we need:
## $HPClBHi: upper mass threshold
## => metaData$hpcLimits["maxMass"]
## $HPClBLo: lower mass threshold
## => metaData$hpcLimits["minMass"]
## $HPClOrd: polynomial order
## => metaData$hpcOrder
## $HPClUse: maybe using of HPC? (seems always be "yes" in our test data)
## => metaData$hpcUse
## $HPCStr: polynomial coefficients in a string
## => metaData$hpcCoefficients
##
## we try to import [optional]:
## DATATYPE
## SPECTROMETER/DATASYSTEM
## => metaData$dataSystem
## .SPECTROMETER TYPE
## => metaData$spectrometerType
## .INLET
## => metaData$inlet
## .IONIZATION MODE
## => metaData$ionizationMode
## $DATE
## => metaData$date
## $ACQMETH
## => metaData$acquisitionMethod
## $AQ_DATE
## => metaData$acquisitionDate
## $AQ_mod
## => metaData$acquisitionMode
## $AQOP_mod
## => metaData$acquisitionOperatorMode
## => metaData$tofMode (replaces file path based method)
## $ATTEN
## => metaData$laserAttenuation
## $COM[1:4]
## => metaData$comments
## $DEFLON
## => metaData$deflection
## $DIGTYP
## => metaData$digitizerType
## $DPCAL1
## => metaData$deflectionPulserCal1
## $DPMASS
## => metaData$deflectionPulserMass
## $FCVer
## => metaData$flexControlVersion
## $ID_raw
## => metaData$id
## $INSTRUM
## => metaData$instrument
## $InstrID
## => metaData$instrumentId
## $InstrTyp
## => metaData$instrumentType
## $Masserr
## => metaData$massError
## $NoSHOTS: number of laser shots
## => metaData$laserShots
## $SPType
## => metaData$spectrumType
## $PATCHNO: sample position on target
## => metaData$patch
## $PATH: original file path (on Bruker flex series controller PC)
## => metaData$path
## $REPHZ
## => metaData$laserRepetition
## $SPOTNO: same as $PATCHNO (in older files often empty, that's why we use
## $PATCHNO instead)
## => metaData$spot
## $TgIDS: target ids
## => metaData$targetIdString
## $TgCount: number of measurement with this target
## => metaData$targetCount
## $TgSer: target serial number
## => metaData$targetSerialNumber
## $TgTyp: target type number
## => metaData$targetTypeNumber
##
## import from file path:
## full current path to fid file:
## => metaData$fidFile
## sample name
## => metaData$sampleName
##
.readAcquFile <- function(fidFile, verbose=FALSE) {
acquFile <- sub(pattern="fid$", x=fidFile, replacement="acqu")
acquFiles <- c(acquFile, paste0(acquFile, "s"))
acquFile <- acquFiles[which.max(file.exists(acquFiles))]
if (!file.exists(acquFile)) {
stop("File ", sQuote(acquFile), " doesn't exists!")
}
if (verbose) {
message("Reading metadata from ", sQuote(acquFile), " ...")
}
con <- file(acquFile, "rt")
acquLines <- readLines(con, n=-1)
close(con)
## collect data
metaData <- list()
## endianness
isBigEndian <- as.integer(.grepAcquValue("##\\$BYTORDA=", acquLines)) == 1L
metaData$byteOrder <- ifelse(isBigEndian, "big", "little")
## obligate
metaData$number <- as.double(.grepAcquValue("##\\$TD=", acquLines))
metaData$timeDelay <- .grepAcquDoubleValue("##\\$DELAY=", acquLines)
metaData$timeDelta <- .grepAcquDoubleValue("##\\$DW=", acquLines)
metaData$calibrationConstants <-
c(c1=.grepAcquDoubleValue("##\\$ML1=", acquLines),
c2=.grepAcquDoubleValue("##\\$ML2=", acquLines),
c3=.grepAcquDoubleValue("##\\$ML3=", acquLines))
## obligate HPC
metaData$hpcLimits <-
c(minMass=.grepAcquDoubleValue("##\\$HPClBLo=", acquLines),
maxMass=.grepAcquDoubleValue("##\\$HPClBHi=", acquLines))
metaData$hpcOrder <- as.double(.grepAcquValue("##\\$HPClOrd=", acquLines))
metaData$hpcUse <-
as.logical(.grepAcquValue("##\\$HPClUse=", acquLines) == "yes")
## was HPC involved? metaData$hpcUse seems to be always true
isHPCused <- isTRUE(metaData$hpcUse &&
metaData$hpcLimits["maxMass"] > 0L &&
metaData$hpcLimits["minMass"] > 0L &&
metaData$hpcOrder > 0L)
if (isHPCused) {
hpcStr <- .grepAcquValue("##\\$HPCStr=", acquLines)
hpcConstants <- .extractHPCConstants(hpcStr)
metaData$hpcCoefficients <- hpcConstants$coefficients
metaData$hpcCalibrationConstant0 <- hpcConstants$calibrationConstant0
metaData$hpcCalibrationConstant2 <- hpcConstants$calibrationConstant2
}
# https://github.com/sgibb/MALDIquantForeign/issues/19
# https://github.com/sgibb/readBrukerFlexData/issues/3
metaData$v1tofCalibration <-
grepl("V1.0CTOF2CalibrationConstants",
.grepAcquValue("##\\$NTBCal=", acquLines))
metaData$v1tofCalibrationConstants <-
.extractV10CTOF2CalibrationConstants(
.grepAcquValue("##\\$NTBCal=", acquLines)
)
## obligate LIFT
metaData$lift <- c(.grepAcquDoubleValue("##\\$Lift1=", acquLines),
.grepAcquDoubleValue("##\\$Lift2=", acquLines))
metaData$tlift <- .grepAcquDoubleValue("##\\$TLift=", acquLines)
## optional
metaData$dataType <- .grepAcquValue("##DATATYPE=", acquLines)
metaData$dataSystem <- .grepAcquValue("##SPECTROMETER/DATASYSTEM=", acquLines)
metaData$spectrometerType <-
.grepAcquValue("##.SPECTROMETER TYPE=", acquLines)
metaData$inlet <- .grepAcquValue("##.INLET=", acquLines)
metaData$ionizationMode <- .grepAcquValue("##.IONIZATION MODE=", acquLines)
metaData$date <- .grepAcquValue("##\\$DATE=", acquLines)
metaData$acquisitionMethod <- .grepAcquValue("##\\$ACQMETH=", acquLines)
metaData$acquisitionDate <- .grepAcquValue("##\\$AQ_DATE=", acquLines)
aq_mod <- .grepAcquValue("##\\$AQ_mod=", acquLines)
if (length(aq_mod)) {
metaData$acquisitionMode <- switch(aq_mod,
"0" = { "qf" },
"1" = { "qsim" },
"2" = { "qseq" },
{ aq_mod }
)
}
aqop <- .grepAcquValue("##\\$AQOP_m=", acquLines)
if (length(aqop)) {
metaData$tofMode <- switch(aqop,
"0" = { "LINEAR" },
"1" = { "REFLECTOR" },
{ aqop }
)
}
metaData$acquisitionOperatorMode <- metaData$tofMode
metaData$laserAttenuation <- .grepAcquDoubleValue("##\\$ATTEN=", acquLines)
metaData$comments <- .grepAcquValue("##\\$CMT.*=", acquLines)
metaData$deflection <-
as.logical(.grepAcquValue("##\\$DEFLON=", acquLines) == "yes")
digtyp <- .grepAcquValue("##\\$DIGTYP=", acquLines)
if (length(digtyp)) {
metaData$digitizerType <- switch(digtyp,
"0" = { "unknown" },
"1" = { "Lecroy LSA1000" },
"2" = { "Acqiris DP105" },
"3" = { "Acqiris DP110" },
"4" = { "Acqiris DP211" },
"5" = { "Acqiris DP240" },
"6" = { "Acqiris AP200" },
"7" = { "Acqiris AP240" },
"8" = { "Acqiris DC440" },
"9" = { "Acqiris DC282" },
"10" = { "Acqiris Unknown subtype" },
"11" = { "Gage" },
"12" = { "Simulator" },
"13" = { "Lecroy WaveRunner" },
"14" = { "Acqiris U1084A" },
"15" = { "NI 5154" },
"16" = { "LeCroy LSA2000" },
"17" = { "Acqiris DP1400" },
"18" = { "NI 5155" },
"19" = { "Bruker BD0G5" },
{ digtyp }
)
}
metaData$deflectionPulserCal1 <-
.grepAcquDoubleValue("##\\$DPCAL1=", acquLines)
metaData$deflectionPulserMass <-
.grepAcquDoubleValue("##\\$DPMASS=", acquLines)
metaData$flexControlVersion <- .grepAcquValue("##\\$FCVer=", acquLines)
metaData$id <- .grepAcquValue("##\\$ID_raw=", acquLines)
metaData$instrument <- .grepAcquValue("##\\$INSTRUM=", acquLines)
metaData$instrumentId <- .grepAcquValue("##\\$InstrID=", acquLines)
instrumentType <- .grepAcquValue("##\\$InstTyp=", acquLines)
if (length(instrumentType)) {
metaData$instrumentType <- switch(instrumentType,
"0" = { "autoflex" },
"1" = { "ultraflex" },
"2" = { "ultraflexTOF/TOF" },
"3" = { "reflex" },
"4" = { "biflex" },
"5" = { "omniflex" },
"6" = { "genoflex" },
"7" = { "massarray" },
"8" = { "autoflexTOF/TOF" },
"9" = { "microflex" },
"10" = { "MT10" },
{ instrumentType }
)
}
metaData$massError <- .grepAcquDoubleValue("##\\$Masserr=", acquLines)
metaData$laserShots <- as.double(.grepAcquValue("##\\$NoSHOTS=", acquLines))
if (metaData$laserShots == 0L) {
warning("File ", sQuote(fidFile), " seems to be empty because ",
"no laser shots applied to this sample.")
}
metaData$patch <- .grepAcquValue("##\\$PATCHNO=", acquLines)
## imaging data
if (length(metaData$patch) &&
grepl(pattern="(R[0-9]+)?X[0-9]+Y[0-9]+", x=metaData$patch,
ignore.case=TRUE)) {
rx <- gregexpr(pattern="[XY][0-9]+", text=metaData$patch)[[1L]]
pos <- substring(metaData$patch, rx+1L, rx+attr(rx, "match.length")-1L)
if (length(pos) == 2L) {
pos <- as.double(pos)
metaData$imaging <- list(pos=c(x=pos[1L], y=pos[2L]))
}
}
metaData$path <- .grepAcquValue("##\\$PATH=", acquLines)
metaData$laserRepetition <- .grepAcquDoubleValue("##\\$REPHZ=", acquLines)
metaData$spot <- .grepAcquValue("##\\$SPOTNO=", acquLines)
sptype <- .grepAcquValue("##\\$SPType=", acquLines)
if (length(sptype)) {
metaData$spectrumType <- switch(sptype,
"0" = { "TOF" },
"1" = { "PSD" },
"2" = { "LIFT" },
"3" = { "PSDSegment" },
{ sptype }
)
}
metaData$targetCount <- as.double(.grepAcquValue("##\\$TgCount", acquLines))
metaData$targetIdString <- .grepAcquValue("##\\$TgIDS", acquLines)
metaData$targetSerialNumber <- .grepAcquValue("##\\$TgSer", acquLines)
metaData$targetTypeNumber <- .grepAcquValue("##\\$TgTyp", acquLines)
metaData$file <- fidFile
metaData$sampleName <- .sampleName(fidFile)
metaData$fullName <- paste(metaData$sampleName, metaData$patch, sep=".")
metaData$name <- metaData$fullName
metaData
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.