R/components-openms.R
In rickhelmus/patRoon: Workflows for Mass-Spectrometry Based Non-Target Analysis
Defines functions
defaultOpenMSAdducts
getOpenMSMADCommand
Documented in
defaultOpenMSAdducts
#' @include main.R
#' @include components-features.R
NULL
#' @rdname components-class
#' @export
componentsOpenMS <- setClass("componentsOpenMS", contains = "componentsFeatures")
setMethod("initialize", "componentsOpenMS",
function(.Object, ...) callNextMethod(.Object, algorithm = "openms", ...))
#' Componentization of adducts, isotopes etc. with OpenMS
#'
#' Uses the
#' \href{https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_MetaboliteAdductDecharger.html}{MetaboliteAdductDecharger}
#' utility (see \url{http://www.openms.de}) to generate components.
#'
#' @templateVar algo OpenMS
#' @templateVar do generate components
#' @templateVar generic generateComponents
#' @templateVar algoParam openms
#' @template algo_generator
#'
#' @details Features that show highly similar chromatographic elution profiles are grouped, and subsequently annotated
#' with their adducts.
#'
#' @param chargeMin,chargeMax The minimum/maximum charge to consider. Corresponds to the
#' \command{algorithm:MetaboliteFeatureDeconvolution:charge_min}/\command{algorithm:MetaboliteFeatureDeconvolution:charge_min}
#' options.
#' @param chargeSpan The maximum charge span for a single analyte. Corresponds to
#' \command{algorithm:MetaboliteFeatureDeconvolution:charge_span_max}.
#' @param qTry Sets how charges are determined. Corresponds to \command{algorithm:MetaboliteFeatureDeconvolution:q_try}.
#' Valid options are \code{"heuristic"} and \code{"all"} (the \code{"feature"} option from \command{OpenMS} is
#' currently not supported).
#' @param potentialAdducts The adducts to consider. Should be a \code{numeric} vector with probabilities for each
#' adduct, \emph{e.g.} \code{potentialAdducts=c("[M+H]+" = 0.8, "[M+Na]+" = 0.2)}. Note that the sum of probabilities
#' should always be \samp{1}. Furthermore, note that additions of multiple adducts should be controlled by the
#' \code{chargeMin}/\code{chargeMax} arguments (and \emph{not} with \code{potentialAdducts}), \emph{e.g.} if
#' \code{chargeMax=2} then both \code{[M+H]+} and \code{[2M+H]2+} may be considered. Please see the
#' \command{algorithm:MetaboliteFeatureDeconvolution:potential_adducts} option of
#' \href{https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_MetaboliteAdductDecharger.html}{MetaboliteAdductDecharger}
#' for more details. If \code{NULL} then the a default is chosen with \code{\link{defaultOpenMSAdducts}} (which is
#' \emph{not} the same as \command{OpenMS}).
#'
#' \setsWF Should be a \code{list} where each entry specifies the potential adducts for a set. Should either be named
#' with the sets names or follow the same order as \code{sets(fGroups)}. Example:
#' \code{potentialAdducts=list(positive=c("[M+H]+" = 0.8, "[M+Na]+" = 0.2), negative=c("[M-H]-" = 0.8, "[M-H2O-H]-" =
#' 0.2))}
#' @param minRTOverlap,retWindow Sets feature retention tolerances when grouping features. Sets the
#' \command{"algorithm:MetaboliteFeatureDeconvolution:retention_max_diff"} and
#' \command{algorithm:MetaboliteFeatureDeconvolution:min_rt_overlap} options.
#' @param extraOpts Named character vector with extra command line parameters directly passed to
#' \command{MetaboliteAdductDecharger}. Set to \code{NULL} to ignore.
#'
#' @templateVar ion TRUE
#' @templateVar minSize TRUE
#' @templateVar absMzDev \command{algorithm:MetaboliteFeatureDeconvolution:mass_max_diff} option
#' @template compon_algo-args
#'
#' @inheritParams generateComponents
#'
#' @return A \code{\link{componentsFeatures}} derived object.
#'
#' @template compon_gen-feat
#'
#' @templateVar class componentsSet
#' @template compon_gen-sets-merged
#'
#' @templateVar what \code{generateComponentsOpenMS}
#' @template uses-multiProc
#'
#' @references \insertRef{Bielow2010}{patRoon}
#'
#' @templateVar what generateComponentsOpenMS
#' @template main-rd-method
#' @export
setMethod("generateComponentsOpenMS", "featureGroups", function(fGroups, ionization = NULL, chargeMin = 1,
chargeMax = 1, chargeSpan = 3,
qTry = "heuristic",
potentialAdducts = NULL,
minRTOverlap = 0.66, retWindow = 1,
absMzDev = 0.005, minSize = 2,
relMinAdductAbundance = 0.75,
adductConflictsUsePref = TRUE,
NMConflicts = c("preferential", "mostAbundant", "mostIntense"),
prefAdducts = c("[M+H]+", "[M-H]-"),
extraOpts = NULL)
{
ac <- checkmate::makeAssertCollection()
ionization <- checkAndGetIonization(ionization, fGroups, add = ac)
aapply(checkmate::assertCount, . ~ chargeMin + chargeMax + chargeSpan + minSize,
positive = TRUE, fixed = list(add = ac))
checkmate::assertChoice(qTry, c("heuristic", "all"))
checkmate::assertNumeric(potentialAdducts, lower = 0, upper = 1, any.missing = FALSE, min.len = 2,
names = "unique", null.ok = TRUE, add = ac)
aapply(checkmate::assertNumber, . ~ retWindow + absMzDev + relMinAdductAbundance, finite = TRUE, lower = 0,
fixed = list(add = ac))
checkmate::assertNumber(minRTOverlap, lower = 0, upper = 1, add = ac)
checkmate::assertFlag(adductConflictsUsePref, add = ac)
checkmate::assertSubset(NMConflicts, c("preferential", "mostAbundant", "mostIntense"), empty.ok = FALSE, add = ac)
checkmate::assertCharacter(prefAdducts, min.chars = 1, any.missing = FALSE, unique = TRUE, add = ac)
checkmate::assertList(extraOpts, any.missing = FALSE, names = "unique", null.ok = TRUE, add = ac)
checkmate::reportAssertions(ac)
if (is.null(potentialAdducts))
potentialAdducts <- defaultOpenMSAdducts(ionization)
if (!numEQ(sum(potentialAdducts), 1))
stop("The sum of all adduct probabilities should be one.")
anaInfo <- analysisInfo(fGroups)
featTable <- featureTable(fGroups)
padds <- sapply(names(potentialAdducts), as.adduct, simplify = FALSE)
if (any(sapply(padds, slot, "molMult") > 1))
stop("Molecule multiplier of potential adducts should not be >1")
oadds <- sapply(padds, as.character, format = "openms")
charges <- sapply(padds, slot, "charge")
chsign <- if (ionization == "positive") "+" else "-"
pa <- sprintf("%s:%s:%f", oadds, strrep(chsign, abs(charges)), potentialAdducts)
params <- list(ionization = ionization, chargeMin = chargeMin, chargeMax = chargeMax, chargeSpan = chargeSpan,
qTry = qTry, potentialAdducts = pa, minRTOverlap = minRTOverlap,
retWindow = retWindow, absMzDev = absMzDev, extraOpts = extraOpts)
baseHash <- makeHash(params, minSize, relMinAdductAbundance)
printf("Annotating all features with OpenMS for %d analyses ...\n", nrow(anaInfo))
cmdQueue <- lapply(seq_len(nrow(anaInfo)), function(anai)
{
hash <- makeHash(featTable[[anai]], baseHash)
logf <- paste0("mad-", anaInfo$analysis[anai], ".txt")
return(list(hash = hash, fTable = featTable[[anai]], logFile = logf))
})
names(cmdQueue) <- anaInfo$analysis
if (length(cmdQueue) == 0)
return(componentsOpenMS())
featComponents <- executeMultiProcess(cmdQueue, function(cmd, ...)
{
fcmp <- patRoon:::parseAdductConsXMLFile(cmd$outFile)
# prune unassigned features
fcmp <- Filter(function(cmp) nrow(cmp) > 1 || nzchar(cmp$adduct_ion), fcmp)
# convert to data.tables and fix adducts
fcmp <- lapply(fcmp, function(cmp)
{
setDT(cmp)
cmp[, adduct_ion := mapply(adduct_ion, charge,
FUN = function(a, c) as.character(as.adduct(a, format = "openms", charge = c)))]
cmp[, charge := NULL]
})
unlink(cmd[c("inFile", "outFile")]) # remove temporary files, as their size may be considerable
return(fcmp)
}, prepareHandler = function(cmd)
{
inFile <- tempfile(fileext = ".featureXML")
writeFeatureXML(cmd$fTable, "analysis.mzML", inFile, TRUE) # NOTE: dummy input mzML file name --> not needed
outFile <- tempfile(fileext = ".consensusXML")
cmdMAD <- do.call(patRoon:::getOpenMSMADCommand, c(list(inFile = inFile, outFile = outFile), params))
return(c(cmd, list(outFile = outFile), cmdMAD))
}, logSubDir = "openms", cacheName = "componentsOpenMS")
return(componentsOpenMS(fGroups = fGroups, absMzDev = absMzDev, minSize = minSize,
relMinAdductAbundance = relMinAdductAbundance,
adductConflictsUsePref = adductConflictsUsePref, NMConflicts = NMConflicts,
prefAdducts = prefAdducts, featureComponents = featComponents))
})
#' @rdname generateComponentsOpenMS
#' @export
setMethod("generateComponentsOpenMS", "featureGroupsSet", function(fGroups, ionization = NULL, chargeMin = 1,
chargeMax = 1, chargeSpan = 3, qTry = "heuristic",
potentialAdducts = NULL, ...)
{
if (is.null(potentialAdducts))
potentialAdducts <- rep(list(NULL), length(sets(fGroups)))
else
{
checkmate::assertList(potentialAdducts, "numeric", any.missing = FALSE, all.missing = FALSE,
len = length(sets(fGroups)))
checkmate::assert(
checkmate::checkNames(names(potentialAdducts), "unnamed"),
checkmate::checkNames(names(potentialAdducts), "unique", must.include = sets(fGroups)),
.var.name = "potentialAdducts"
)
if (checkmate::testNames(names(potentialAdducts), "unnamed"))
names(potentialAdducts) <- sets(fGroups)
potentialAdducts <- potentialAdducts[sets(fGroups)]
}
generateComponentsSet(fGroups, ionization, generateComponentsOpenMS, setIonization = TRUE, chargeMin = chargeMin,
chargeMax = chargeMax, chargeSpan = chargeSpan, qTry = qTry, ...,
setArgs = lapply(potentialAdducts, function(pa) list(potentialAdducts = pa)))
})
getOpenMSMADCommand <- function(inFile, outFile, ionization, chargeMin, chargeMax, chargeSpan, qTry,
potentialAdducts, minRTOverlap, retWindow, absMzDev, extraOpts)
{
boolToChr <- function(b) if (b) "true" else "false"
if (ionization == "negative")
{
# ensure they are negative
chargeMin <- -abs(chargeMin); chargeMax <- -abs(chargeMax)
}
settings <- list("-algorithm:MetaboliteFeatureDeconvolution:charge_min" = chargeMin,
"-algorithm:MetaboliteFeatureDeconvolution:charge_max" = chargeMax,
"-algorithm:MetaboliteFeatureDeconvolution:charge_span_max" = chargeSpan,
"-algorithm:MetaboliteFeatureDeconvolution:q_try" = qTry,
"-algorithm:MetaboliteFeatureDeconvolution:retention_max_diff" = retWindow,
"-algorithm:MetaboliteFeatureDeconvolution:mass_max_diff" = absMzDev,
"-algorithm:MetaboliteFeatureDeconvolution:min_rt_overlap" = minRTOverlap)
recentMAD <- OpenMSVersionAtLeast("MetaboliteAdductDecharger", "3.0")
if (!recentMAD) # negative_mode param usage was changed in OpenMS 3.0
settings <- c(settings, list("-algorithm:MetaboliteFeatureDeconvolution:negative_mode" = boolToChr(ionization == "negative")))
if (!is.null(extraOpts))
settings <- modifyList(settings, extraOpts)
settingsArgs <- OpenMSArgListToOpts(settings)
if (recentMAD && ionization == "negative")
settingsArgs <- c(settingsArgs, "-algorithm:MetaboliteFeatureDeconvolution:negative_mode")
# add potential adducts later as OpenMSArgListToOpts() doesn't handle this currently...
settingsArgs <- c(settingsArgs, "-algorithm:MetaboliteFeatureDeconvolution:potential_adducts", potentialAdducts)
return(list(command = getExtDepPath("openms", "MetaboliteAdductDecharger"),
args = c(settingsArgs, "-in", inFile, "-out_cm", outFile)))
}
#' Default adducts for OpenMS componentization
#'
#' Returns the default adducts and their probabilities when the OpenMS algorithm is used for componentization.
#'
#' See the \code{potentialAdducts} argument of \code{\link{generateComponentsOpenMS}} for more details.
#'
#' @param ionization The ionization polarity: either \code{"positive"} or \code{"negative"}.
#'
#' @export
defaultOpenMSAdducts <- function(ionization)
{
checkmate::assertChoice(ionization, c("positive", "negative"))
if (ionization == "positive")
return(c("[M+H]+" = 0.4,
"[M+Na]+" = 0.2,
"[M+NH4]+" = 0.2,
"[M+K]+" = 0.1,
"[M-H2O]+" = 0.1))
# UNDONE: more for neg?
return(c("[M-H]-" = 0.8,
"[M-H2O-H]-" = 0.2))
}
rickhelmus/patRoon documentation built on April 25, 2024, 8:15 a.m.
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Defines functions defaultOpenMSAdducts getOpenMSMADCommand
Documented in defaultOpenMSAdducts
#' @include main.R
#' @include components-features.R
NULL
#' @rdname components-class
#' @export
componentsOpenMS <- setClass("componentsOpenMS", contains = "componentsFeatures")
setMethod("initialize", "componentsOpenMS",
function(.Object, ...) callNextMethod(.Object, algorithm = "openms", ...))
#' Componentization of adducts, isotopes etc. with OpenMS
#'
#' Uses the
#' \href{https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_MetaboliteAdductDecharger.html}{MetaboliteAdductDecharger}
#' utility (see \url{http://www.openms.de}) to generate components.
#'
#' @templateVar algo OpenMS
#' @templateVar do generate components
#' @templateVar generic generateComponents
#' @templateVar algoParam openms
#' @template algo_generator
#'
#' @details Features that show highly similar chromatographic elution profiles are grouped, and subsequently annotated
#' with their adducts.
#'
#' @param chargeMin,chargeMax The minimum/maximum charge to consider. Corresponds to the
#' \command{algorithm:MetaboliteFeatureDeconvolution:charge_min}/\command{algorithm:MetaboliteFeatureDeconvolution:charge_min}
#' options.
#' @param chargeSpan The maximum charge span for a single analyte. Corresponds to
#' \command{algorithm:MetaboliteFeatureDeconvolution:charge_span_max}.
#' @param qTry Sets how charges are determined. Corresponds to \command{algorithm:MetaboliteFeatureDeconvolution:q_try}.
#' Valid options are \code{"heuristic"} and \code{"all"} (the \code{"feature"} option from \command{OpenMS} is
#' currently not supported).
#' @param potentialAdducts The adducts to consider. Should be a \code{numeric} vector with probabilities for each
#' adduct, \emph{e.g.} \code{potentialAdducts=c("[M+H]+" = 0.8, "[M+Na]+" = 0.2)}. Note that the sum of probabilities
#' should always be \samp{1}. Furthermore, note that additions of multiple adducts should be controlled by the
#' \code{chargeMin}/\code{chargeMax} arguments (and \emph{not} with \code{potentialAdducts}), \emph{e.g.} if
#' \code{chargeMax=2} then both \code{[M+H]+} and \code{[2M+H]2+} may be considered. Please see the
#' \command{algorithm:MetaboliteFeatureDeconvolution:potential_adducts} option of
#' \href{https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/UTILS_MetaboliteAdductDecharger.html}{MetaboliteAdductDecharger}
#' for more details. If \code{NULL} then the a default is chosen with \code{\link{defaultOpenMSAdducts}} (which is
#' \emph{not} the same as \command{OpenMS}).
#'
#' \setsWF Should be a \code{list} where each entry specifies the potential adducts for a set. Should either be named
#' with the sets names or follow the same order as \code{sets(fGroups)}. Example:
#' \code{potentialAdducts=list(positive=c("[M+H]+" = 0.8, "[M+Na]+" = 0.2), negative=c("[M-H]-" = 0.8, "[M-H2O-H]-" =
#' 0.2))}
#' @param minRTOverlap,retWindow Sets feature retention tolerances when grouping features. Sets the
#' \command{"algorithm:MetaboliteFeatureDeconvolution:retention_max_diff"} and
#' \command{algorithm:MetaboliteFeatureDeconvolution:min_rt_overlap} options.
#' @param extraOpts Named character vector with extra command line parameters directly passed to
#' \command{MetaboliteAdductDecharger}. Set to \code{NULL} to ignore.
#'
#' @templateVar ion TRUE
#' @templateVar minSize TRUE
#' @templateVar absMzDev \command{algorithm:MetaboliteFeatureDeconvolution:mass_max_diff} option
#' @template compon_algo-args
#'
#' @inheritParams generateComponents
#'
#' @return A \code{\link{componentsFeatures}} derived object.
#'
#' @template compon_gen-feat
#'
#' @templateVar class componentsSet
#' @template compon_gen-sets-merged
#'
#' @templateVar what \code{generateComponentsOpenMS}
#' @template uses-multiProc
#'
#' @references \insertRef{Bielow2010}{patRoon}
#'
#' @templateVar what generateComponentsOpenMS
#' @template main-rd-method
#' @export
setMethod("generateComponentsOpenMS", "featureGroups", function(fGroups, ionization = NULL, chargeMin = 1,
chargeMax = 1, chargeSpan = 3,
qTry = "heuristic",
potentialAdducts = NULL,
minRTOverlap = 0.66, retWindow = 1,
absMzDev = 0.005, minSize = 2,
relMinAdductAbundance = 0.75,
adductConflictsUsePref = TRUE,
NMConflicts = c("preferential", "mostAbundant", "mostIntense"),
prefAdducts = c("[M+H]+", "[M-H]-"),
extraOpts = NULL)
{
ac <- checkmate::makeAssertCollection()
ionization <- checkAndGetIonization(ionization, fGroups, add = ac)
aapply(checkmate::assertCount, . ~ chargeMin + chargeMax + chargeSpan + minSize,
positive = TRUE, fixed = list(add = ac))
checkmate::assertChoice(qTry, c("heuristic", "all"))
checkmate::assertNumeric(potentialAdducts, lower = 0, upper = 1, any.missing = FALSE, min.len = 2,
names = "unique", null.ok = TRUE, add = ac)
aapply(checkmate::assertNumber, . ~ retWindow + absMzDev + relMinAdductAbundance, finite = TRUE, lower = 0,
fixed = list(add = ac))
checkmate::assertNumber(minRTOverlap, lower = 0, upper = 1, add = ac)
checkmate::assertFlag(adductConflictsUsePref, add = ac)
checkmate::assertSubset(NMConflicts, c("preferential", "mostAbundant", "mostIntense"), empty.ok = FALSE, add = ac)
checkmate::assertCharacter(prefAdducts, min.chars = 1, any.missing = FALSE, unique = TRUE, add = ac)
checkmate::assertList(extraOpts, any.missing = FALSE, names = "unique", null.ok = TRUE, add = ac)
checkmate::reportAssertions(ac)
if (is.null(potentialAdducts))
potentialAdducts <- defaultOpenMSAdducts(ionization)
if (!numEQ(sum(potentialAdducts), 1))
stop("The sum of all adduct probabilities should be one.")
anaInfo <- analysisInfo(fGroups)
featTable <- featureTable(fGroups)
padds <- sapply(names(potentialAdducts), as.adduct, simplify = FALSE)
if (any(sapply(padds, slot, "molMult") > 1))
stop("Molecule multiplier of potential adducts should not be >1")
oadds <- sapply(padds, as.character, format = "openms")
charges <- sapply(padds, slot, "charge")
chsign <- if (ionization == "positive") "+" else "-"
pa <- sprintf("%s:%s:%f", oadds, strrep(chsign, abs(charges)), potentialAdducts)
params <- list(ionization = ionization, chargeMin = chargeMin, chargeMax = chargeMax, chargeSpan = chargeSpan,
qTry = qTry, potentialAdducts = pa, minRTOverlap = minRTOverlap,
retWindow = retWindow, absMzDev = absMzDev, extraOpts = extraOpts)
baseHash <- makeHash(params, minSize, relMinAdductAbundance)
printf("Annotating all features with OpenMS for %d analyses ...\n", nrow(anaInfo))
cmdQueue <- lapply(seq_len(nrow(anaInfo)), function(anai)
{
hash <- makeHash(featTable[[anai]], baseHash)
logf <- paste0("mad-", anaInfo$analysis[anai], ".txt")
return(list(hash = hash, fTable = featTable[[anai]], logFile = logf))
})
names(cmdQueue) <- anaInfo$analysis
if (length(cmdQueue) == 0)
return(componentsOpenMS())
featComponents <- executeMultiProcess(cmdQueue, function(cmd, ...)
{
fcmp <- patRoon:::parseAdductConsXMLFile(cmd$outFile)
# prune unassigned features
fcmp <- Filter(function(cmp) nrow(cmp) > 1 || nzchar(cmp$adduct_ion), fcmp)
# convert to data.tables and fix adducts
fcmp <- lapply(fcmp, function(cmp)
{
setDT(cmp)
cmp[, adduct_ion := mapply(adduct_ion, charge,
FUN = function(a, c) as.character(as.adduct(a, format = "openms", charge = c)))]
cmp[, charge := NULL]
})
unlink(cmd[c("inFile", "outFile")]) # remove temporary files, as their size may be considerable
return(fcmp)
}, prepareHandler = function(cmd)
{
inFile <- tempfile(fileext = ".featureXML")
writeFeatureXML(cmd$fTable, "analysis.mzML", inFile, TRUE) # NOTE: dummy input mzML file name --> not needed
outFile <- tempfile(fileext = ".consensusXML")
cmdMAD <- do.call(patRoon:::getOpenMSMADCommand, c(list(inFile = inFile, outFile = outFile), params))
return(c(cmd, list(outFile = outFile), cmdMAD))
}, logSubDir = "openms", cacheName = "componentsOpenMS")
return(componentsOpenMS(fGroups = fGroups, absMzDev = absMzDev, minSize = minSize,
relMinAdductAbundance = relMinAdductAbundance,
adductConflictsUsePref = adductConflictsUsePref, NMConflicts = NMConflicts,
prefAdducts = prefAdducts, featureComponents = featComponents))
})
#' @rdname generateComponentsOpenMS
#' @export
setMethod("generateComponentsOpenMS", "featureGroupsSet", function(fGroups, ionization = NULL, chargeMin = 1,
chargeMax = 1, chargeSpan = 3, qTry = "heuristic",
potentialAdducts = NULL, ...)
{
if (is.null(potentialAdducts))
potentialAdducts <- rep(list(NULL), length(sets(fGroups)))
else
{
checkmate::assertList(potentialAdducts, "numeric", any.missing = FALSE, all.missing = FALSE,
len = length(sets(fGroups)))
checkmate::assert(
checkmate::checkNames(names(potentialAdducts), "unnamed"),
checkmate::checkNames(names(potentialAdducts), "unique", must.include = sets(fGroups)),
.var.name = "potentialAdducts"
)
if (checkmate::testNames(names(potentialAdducts), "unnamed"))
names(potentialAdducts) <- sets(fGroups)
potentialAdducts <- potentialAdducts[sets(fGroups)]
}
generateComponentsSet(fGroups, ionization, generateComponentsOpenMS, setIonization = TRUE, chargeMin = chargeMin,
chargeMax = chargeMax, chargeSpan = chargeSpan, qTry = qTry, ...,
setArgs = lapply(potentialAdducts, function(pa) list(potentialAdducts = pa)))
})
getOpenMSMADCommand <- function(inFile, outFile, ionization, chargeMin, chargeMax, chargeSpan, qTry,
potentialAdducts, minRTOverlap, retWindow, absMzDev, extraOpts)
{
boolToChr <- function(b) if (b) "true" else "false"
if (ionization == "negative")
{
# ensure they are negative
chargeMin <- -abs(chargeMin); chargeMax <- -abs(chargeMax)
}
settings <- list("-algorithm:MetaboliteFeatureDeconvolution:charge_min" = chargeMin,
"-algorithm:MetaboliteFeatureDeconvolution:charge_max" = chargeMax,
"-algorithm:MetaboliteFeatureDeconvolution:charge_span_max" = chargeSpan,
"-algorithm:MetaboliteFeatureDeconvolution:q_try" = qTry,
"-algorithm:MetaboliteFeatureDeconvolution:retention_max_diff" = retWindow,
"-algorithm:MetaboliteFeatureDeconvolution:mass_max_diff" = absMzDev,
"-algorithm:MetaboliteFeatureDeconvolution:min_rt_overlap" = minRTOverlap)
recentMAD <- OpenMSVersionAtLeast("MetaboliteAdductDecharger", "3.0")
if (!recentMAD) # negative_mode param usage was changed in OpenMS 3.0
settings <- c(settings, list("-algorithm:MetaboliteFeatureDeconvolution:negative_mode" = boolToChr(ionization == "negative")))
if (!is.null(extraOpts))
settings <- modifyList(settings, extraOpts)
settingsArgs <- OpenMSArgListToOpts(settings)
if (recentMAD && ionization == "negative")
settingsArgs <- c(settingsArgs, "-algorithm:MetaboliteFeatureDeconvolution:negative_mode")
# add potential adducts later as OpenMSArgListToOpts() doesn't handle this currently...
settingsArgs <- c(settingsArgs, "-algorithm:MetaboliteFeatureDeconvolution:potential_adducts", potentialAdducts)
return(list(command = getExtDepPath("openms", "MetaboliteAdductDecharger"),
args = c(settingsArgs, "-in", inFile, "-out_cm", outFile)))
}
#' Default adducts for OpenMS componentization
#'
#' Returns the default adducts and their probabilities when the OpenMS algorithm is used for componentization.
#'
#' See the \code{potentialAdducts} argument of \code{\link{generateComponentsOpenMS}} for more details.
#'
#' @param ionization The ionization polarity: either \code{"positive"} or \code{"negative"}.
#'
#' @export
defaultOpenMSAdducts <- function(ionization)
{
checkmate::assertChoice(ionization, c("positive", "negative"))
if (ionization == "positive")
return(c("[M+H]+" = 0.4,
"[M+Na]+" = 0.2,
"[M+NH4]+" = 0.2,
"[M+K]+" = 0.1,
"[M-H2O]+" = 0.1))
# UNDONE: more for neg?
return(c("[M-H]-" = 0.8,
"[M-H2O-H]-" = 0.2))
}
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