Nothing
R/methods-OnDiskMSnExp.R
In xcms: LC-MS and GC-MS Data Analysis
Defines functions
.peaks_to_result
## Methods for MSnbase's OnDiskMSnExp and MSnExp objects.
#' @include DataClasses.R functions-OnDiskMSnExp.R do_findChromPeaks-functions.R
## Main roxygen documentation for the centWace feature detection is in
## DataClasses, before the definition of the CentWaveParam class.
## The centWave peak detection method for OnDiskMSnExp:
#' @title Chromatographic peak detection using the centWave method
#'
#' @description The \code{detectChromPeaks,OnDiskMSnExp,CentWaveParam} method
#' performs chromatographic peak detection using the \emph{centWave}
#' algorithm on all samples from an \code{\link{OnDiskMSnExp}}
#' object. \code{\link{OnDiskMSnExp}} objects encapsule all
#' experiment specific data and load the spectra data (mz and intensity
#' values) on the fly from the original files applying also all eventual
#' data manipulations.
#'
#' @details Parallel processing (one process per sample) is supported and can
#' be configured either by the \code{BPPARAM} parameter or by globally
#' defining the parallel processing mode using the
#' \code{\link{register}} method from the \code{BiocParallel}
#' package.
#'
#' @param object For \code{findChromPeaks}: an
#' \code{\link{OnDiskMSnExp}} object containing the MS- and all
#' other experiment-relevant data.
#'
#' For all other methods: a parameter object.
#'
#' @param param An \code{CentWaveParam} object containing all settings for the
#' centWave algorithm.
#'
#' @param BPPARAM A parameter class specifying if and how parallel processing
#' should be performed. It defaults to \code{\link{bpparam}}.
#' See documentation of the \code{BiocParallel} for more details. If
#' parallel processing is enabled, peak detection is performed in parallel
#' on several of the input samples.
#'
#' @param return.type Character specifying what type of object the method should
#' return. Can be either \code{"XCMSnExp"} (default), \code{"list"} or
#' \code{"xcmsSet"}.
#'
#' @param msLevel \code{integer(1)} defining the MS level on which the peak
#' detection should be performed. Defaults to \code{msLevel = 1}.
#'
#' @return For \code{findChromPeaks}: if \code{return.type = "XCMSnExp"} an
#' \code{\link{XCMSnExp}} object with the results of the peak detection.
#' If \code{return.type = "list"} a list of length equal to the number of
#' samples with matrices specifying the identified peaks.
#' If \code{return.type = "xcmsSet"} an \code{\linkS4class{xcmsSet}} object
#' with the results of the peak detection.
#'
#' @seealso \code{\link{XCMSnExp}} for the object containing the results of
#' the peak detection.
#'
#' @rdname findChromPeaks-centWave
setMethod("findChromPeaks",
signature(object = "OnDiskMSnExp", param = "CentWaveParam"),
function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
msLevel = 1L) {
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported", call. = FALSE)
## Check if the data is centroided
centroided <- all(centroided(object)[msLevel(object) %in% msLevel])
if (is.na(centroided)) {
idx <- which(msLevel(object) %in% msLevel)
idx <- idx[ceiling(length(idx) / 3)]
suppressWarnings(
centroided <- isCentroided(object[[idx]])
)
}
if (is.na(centroided) || !centroided)
warning("Your data appears to be not centroided! CentWave",
" works best on data in centroid mode.")
resList <- bplapply(.split_by_file2(object, msLevel. = msLevel),
FUN = findChromPeaks_OnDiskMSnExp,
method = "centWave",
param = param, BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
fnames = fileNames(object))
if (return.type == "list")
return(res$peaks)
object <- .peaks_to_result(res, object, startDate, param, msLevel)
if (return.type == "xcmsSet")
as(object, "xcmsSet")
else object
})
## The matchedFilter peak detection method for OnDiskMSnExp:
#' @title Peak detection in the chromatographic time domain
#'
#' @description The \code{findChromPeaks,OnDiskMSnExp,MatchedFilterParam}
#' method performs peak detection using the \emph{matchedFilter} algorithm
#' on all samples from an \code{\link{OnDiskMSnExp}} object.
#' \code{\link{OnDiskMSnExp}} objects encapsule all experiment
#' specific data and load the spectra data (mz and intensity values) on the
#' fly from the original files applying also all eventual data
#' manipulations.
#'
#' @details Parallel processing (one process per sample) is supported and can
#' be configured either by the \code{BPPARAM} parameter or by globally
#' defining the parallel processing mode using the
#' \code{\link{register}} method from the \code{BiocParallel}
#' package.
#'
#' @param object For \code{findChromPeaks}: an
#' \code{\link{OnDiskMSnExp}} object containing the MS- and all
#' other experiment-relevant data.
#'
#' For all other methods: a parameter object.
#'
#' @param param An \code{MatchedFilterParam} object containing all settings for
#' the matchedFilter algorithm.
#'
#' @inheritParams findChromPeaks-centWave
#'
#' @return For \code{findChromPeaks}: if \code{return.type = "XCMSnExp"} an
#' \code{\link{XCMSnExp}} object with the results of the peak detection.
#' If \code{return.type = "list"} a list of length equal to the number of
#' samples with matrices specifying the identified peaks.
#' If \code{return.type = "xcmsSet"} an \code{\linkS4class{xcmsSet}} object
#' with the results of the peak detection.
#'
#' @seealso \code{\link{XCMSnExp}} for the object containing the results of
#' the chromatographic peak detection.
#'
#' @rdname findChromPeaks-matchedFilter
setMethod("findChromPeaks",
signature(object = "OnDiskMSnExp", param = "MatchedFilterParam"),
function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
msLevel = 1L) {
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported")
resList <- bplapply(.split_by_file2(object, msLevel. = msLevel),
FUN = findChromPeaks_OnDiskMSnExp,
method = "matchedFilter",
param = param,
BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
fnames = fileNames(object))
if (return.type == "list")
return(res$peaks)
object <- .peaks_to_result(res, object, startDate, param, msLevel)
if (return.type == "xcmsSet")
as(object, "xcmsSet")
else object
})
#' Simple helper function to convert the peak finding results to an XCMSnExp
#' result object.
#'
#' @noRd
.peaks_to_result <- function(res, object, startDate, param, msLevel) {
xph <- XProcessHistory(param = param, date. = startDate,
type. = .PROCSTEP.PEAK.DETECTION,
fileIndex = 1:length(fileNames(object)),
msLevel = msLevel)
object <- as(object, "XCMSnExp")
phist <- object@.processHistory
## if (hasAdjustedRtime(object) | hasFeatures(object))
## object@msFeatureData <- new("MsFeatureData")
pks <- do.call(rbind, res$peaks)
if (length(pks) > 0) {
chromPeaks(object) <- pks
chromPeakData(object)$ms_level <- as.integer(msLevel)
chromPeakData(object)$is_filled <- FALSE
}
object@.processHistory <- c(phist, list(xph))
validObject(object)
object
}
## massifquant
## The massifquant peak detection method for OnDiskMSnExp:
#' @title Chromatographic peak detection using the massifquant method
#'
#' @description The \code{findChromPeaks,OnDiskMSnExp,MassifquantParam}
#' method performs chromatographic peak detection using the
#' \emph{massifquant} algorithm on all samples from an
#' \code{\link{OnDiskMSnExp}} object.
#' \code{\link{OnDiskMSnExp}} objects encapsule all experiment
#' specific data and load the spectra data (mz and intensity values) on the
#' fly from the original files applying also all eventual data
#' manipulations.
#'
#' @details Parallel processing (one process per sample) is supported and can
#' be configured either by the \code{BPPARAM} parameter or by globally
#' defining the parallel processing mode using the
#' \code{\link{register}} method from the \code{BiocParallel}
#' package.
#'
#' @param object For \code{findChromPeaks}: an
#' \code{\link{OnDiskMSnExp}} object containing the MS- and all
#' other experiment-relevant data.
#'
#' For all other methods: a parameter object.
#'
#' @param param An \code{MassifquantParam} object containing all settings for
#' the massifquant algorithm.
#'
#' @inheritParams findChromPeaks-centWave
#'
#' @return For \code{findChromPeaks}: if \code{return.type = "XCMSnExp"} an
#' \code{\link{XCMSnExp}} object with the results of the peak detection.
#' If \code{return.type = "list"} a list of length equal to the number of
#' samples with matrices specifying the identified peaks.
#' If \code{return.type = "xcmsSet"} an \code{\linkS4class{xcmsSet}} object
#' with the results of the peak detection.
#'
#' @seealso \code{\link{XCMSnExp}} for the object containing the results of
#' the peak detection.
#'
#' @rdname findChromPeaks-massifquant
setMethod("findChromPeaks",
signature(object = "OnDiskMSnExp", param = "MassifquantParam"),
function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
msLevel = 1L) {
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported")
resList <- bplapply(.split_by_file2(object, msLevel. = msLevel),
FUN = findChromPeaks_OnDiskMSnExp,
method = "massifquant", param = param,
BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
fnames = fileNames(object))
if (return.type == "list")
return(res$peaks)
object <- .peaks_to_result(res, object, startDate, param, msLevel)
if (return.type == "xcmsSet")
as(object, "xcmsSet")
else object
})
## MSW
## The MSW peak detection method for OnDiskMSnExp:
#' @title Single-spectrum non-chromatography MS data peak detection
#'
#' @description The \code{findChromPeaks,OnDiskMSnExp,MSWParam}
#' method performs peak detection in single-spectrum non-chromatography MS
#' data using functionality from the \code{MassSpecWavelet} package on all
#' samples from an \code{\link{OnDiskMSnExp}} object.
#' \code{\link{OnDiskMSnExp}} objects encapsule all experiment
#' specific data and load the spectra data (mz and intensity values) on the
#' fly from the original files applying also all eventual data
#' manipulations.
#'
#' @details Parallel processing (one process per sample) is supported and can
#' be configured either by the \code{BPPARAM} parameter or by globally
#' defining the parallel processing mode using the
#' \code{\link{register}} method from the \code{BiocParallel}
#' package.
#'
#' @param object For \code{findChromPeaks}: an
#' \code{\link{OnDiskMSnExp}} object containing the MS- and all
#' other experiment-relevant data.
#'
#' For all other methods: a parameter object.
#'
#' @param param An \code{MSWParam} object containing all settings for
#' the algorithm.
#'
#' @inheritParams findChromPeaks-centWave
#'
#' @return For \code{findChromPeaks}: if \code{return.type = "XCMSnExp"} an
#' \code{\link{XCMSnExp}} object with the results of the peak detection.
#' If \code{return.type = "list"} a list of length equal to the number of
#' samples with matrices specifying the identified peaks.
#' If \code{return.type = "xcmsSet"} an \code{\linkS4class{xcmsSet}} object
#' with the results of the detection.
#'
#' @seealso \code{\link{XCMSnExp}} for the object containing the results of
#' the peak detection.
#'
#' @rdname findPeaks-MSW
setMethod("findChromPeaks",
signature(object = "OnDiskMSnExp", param = "MSWParam"),
function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
msLevel = 1L) {
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported")
object_mslevel <- filterMsLevel(object, msLevel. = msLevel)
if (length(object_mslevel) == 0)
stop("No MS level ", msLevel, " spectra present to perform ",
"peak detection")
rts <- split(rtime(object_mslevel),
f = as.factor(fromFile(object_mslevel)))
if (any(lengths(rts) > 1))
stop("The MSW method can only be applied to single spectrum,",
" non-chromatographic, files (i.e. with a single ",
"retention time).")
resList <- bplapply(.split_by_file2(object_mslevel),
FUN = findPeaks_MSW_OnDiskMSnExp,
method = "MSW", param = param,
BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
fnames = fileNames(object_mslevel))
if (return.type == "list")
return(res$peaks)
object <- .peaks_to_result(res, object, startDate, param, msLevel)
if (return.type == "xcmsSet")
as(object, "xcmsSet")
else object
})
## The centWave with predicted isotope peak detection method for OnDiskMSnExp:
#' @title Two-step centWave peak detection considering also isotopes
#'
#' @description The \code{findChromPeaks,OnDiskMSnExp,CentWavePredIsoParam}
#' method performs a two-step centWave-based chromatographic peak detection
#' on all samples from an \code{\link{OnDiskMSnExp}} object.
#' \code{\link{OnDiskMSnExp}} objects encapsule all experiment
#' specific data and load the spectra data (mz and intensity values) on the
#' fly from the original files applying also all eventual data
#' manipulations.
#'
#' @details Parallel processing (one process per sample) is supported and can
#' be configured either by the \code{BPPARAM} parameter or by globally
#' defining the parallel processing mode using the
#' \code{\link{register}} method from the \code{BiocParallel}
#' package.
#'
#' @param param An \code{CentWavePredIsoParam} object with the settings for the
#' chromatographic peak detection algorithm.
#'
#' @inheritParams findChromPeaks-centWave
#'
#' @return For \code{findChromPeaks}: if \code{return.type = "XCMSnExp"} an
#' \code{\link{XCMSnExp}} object with the results of the peak detection.
#' If \code{return.type = "list"} a list of length equal to the number of
#' samples with matrices specifying the identified peaks.
#' If \code{return.type = "xcmsSet"} an \code{\linkS4class{xcmsSet}} object
#' with the results of the peak detection.
#'
#' @seealso \code{\link{XCMSnExp}} for the object containing the results of
#' the peak detection.
#'
#' @rdname findChromPeaks-centWaveWithPredIsoROIs
setMethod("findChromPeaks",
signature(object = "OnDiskMSnExp", param = "CentWavePredIsoParam"),
function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
msLevel = 1L) {
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported")
## Check if the data is centroided
centroided <- all(centroided(object)[msLevel(object) %in% msLevel])
if (is.na(centroided)) {
idx <- which(msLevel(object) %in% msLevel)
idx <- idx[ceiling(length(idx) / 3)]
suppressWarnings(
centroided <- isCentroided(object[[idx]])
)
}
if (is.na(centroided) || !centroided)
warning("Your data appears to be not centroided! CentWave",
" works best on data in centroid mode.")
resList <- bplapply(.split_by_file2(object, msLevel. = msLevel),
FUN = findChromPeaks_OnDiskMSnExp,
method = "centWaveWithPredIsoROIs",
param = param, BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
fnames = fileNames(object))
if (return.type == "list")
return(res$peaks)
object <- .peaks_to_result(res, object, startDate, param, msLevel)
if (return.type == "xcmsSet")
as(object, "xcmsSet")
else object
})
## profMat method for XCMSnExp/OnDiskMSnExp.
#' @description \code{profMat}: creates a \emph{profile matrix}, which
#' is a n x m matrix, n (rows) representing equally spaced m/z values (bins)
#' and m (columns) the retention time of the corresponding scans. Each cell
#' contains the maximum intensity measured for the specific scan and m/z
#' values. See \code{\link{profMat}} for more details and description of
#' the various binning methods.
#'
#' @param ... Additional parameters.
#'
#' @return For \code{profMat}: a \code{list} with a the profile matrix
#' \code{matrix} (or matrices if \code{fileIndex} was not specified or if
#' \code{length(fileIndex) > 1}). See \code{\link{profile-matrix}} for
#' general help and information about the profile matrix.
#'
#' @inheritParams profMat-xcmsSet
#'
#' @rdname XCMSnExp-class
setMethod("profMat", signature(object = "OnDiskMSnExp"), function(object,
method = "bin",
step = 0.1,
baselevel = NULL,
basespace = NULL,
mzrange. = NULL,
fileIndex,
...) {
## Subset the object by fileIndex.
if (!missing(fileIndex)) {
if (!is.numeric(fileIndex))
stop("'fileIndex' has to be an integer.")
if (!all(fileIndex %in% seq_along(fileNames(object))))
stop("'fileIndex' has to be an integer between 1 and ",
length(fileNames(object)), "!")
object <- filterFile(object, fileIndex)
}
## Split it by file and bplapply over it to generate the profile matrix.
theF <- factor(seq_along(fileNames(object)))
theDots <- list(...)
if (any(names(theDots) == "returnBreaks"))
returnBreaks <- theDots$returnBreaks
else
returnBreaks <- FALSE
res <- bplapply(splitByFile(object, f = theF), function(z, bmethod, bstep,
bbaselevel,
bbasespace,
bmzrange.,
breturnBreaks) {
require(xcms, quietly = TRUE)
sps <- spectra(z, BPPARAM = SerialParam())
mzs <- lapply(sps, mz)
## Fix for issue #301: got spectra with m/z being NA.
if (any(is.na(unlist(mzs, use.names = FALSE)))) {
sps <- lapply(sps, clean, all = TRUE)
mzs <- lapply(sps, mz)
}
## Fix for issue #312: remove empty spectra, that we are however adding
## later so that the ncol(profMat) == length(rtime(object))
pk_count <- lengths(mzs)
empty_spectra <- which(pk_count == 0)
if (length(empty_spectra)) {
mzs <- mzs[-empty_spectra]
sps <- sps[-empty_spectra]
}
vps <- lengths(mzs, use.names = FALSE)
res <- .createProfileMatrix(mz = unlist(mzs, use.names = FALSE),
int = unlist(lapply(sps, intensity),
use.names = FALSE),
valsPerSpect = vps,
method = bmethod,
step = bstep,
baselevel = bbaselevel,
basespace = bbasespace,
mzrange. = bmzrange.,
returnBreaks = breturnBreaks)
if (length(empty_spectra))
if (returnBreaks)
res$profMat <- .insertColumn(res$profMat, empty_spectra, 0)
else
res <- .insertColumn(res, empty_spectra, 0)
res
}, bmethod = method, bstep = step, bbaselevel = baselevel,
bbasespace = basespace, bmzrange. = mzrange., breturnBreaks = returnBreaks)
res
})
#' @rdname adjustRtime-obiwarp
setMethod("adjustRtime",
signature(object = "OnDiskMSnExp", param = "ObiwarpParam"),
function(object, param, msLevel = 1L) {
## Filter for MS level, perform adjustment and if the object
## contains spectra from other MS levels too, adjust all raw
## rts based on the difference between adjusted and raw rts.
object_sub <- filterMsLevel(object, msLevel = msLevel)
if (length(object_sub) == 0)
stop("No spectra of MS level ", msLevel, " present")
res <- .obiwarp(object_sub, param = param)
## Adjust the retention time for spectra of all MS levels, if
## if there are some other than msLevel (issue #214).
if (length(unique(msLevel(object))) !=
length(unique(msLevel(object_sub)))) {
message("Apply retention time correction performed on MS",
msLevel, " to spectra from all MS levels")
## I need raw and adjusted rt for the adjusted spectra
## and the raw rt of all.
rtime_all <- split(rtime(object), fromFile(object))
rtime_sub <- split(rtime(object_sub), fromFile(object_sub))
## For loop is faster than lapply. No sense to do parallel
for (i in 1:length(rtime_all)) {
n_vals <- length(rtime_sub[[i]])
idx_below <- which(rtime_all[[i]] < rtime_sub[[i]][1])
if (length(idx_below))
vals_below <- rtime_all[[i]][idx_below]
idx_above <- which(rtime_all[[i]] >
rtime_sub[[i]][n_vals])
if (length(idx_above))
vals_above <- rtime_all[[i]][idx_above]
## Adjust the retention time. Note: this should be
## OK even if values are not sorted.
adj_fun <- approxfun(x = rtime_sub[[i]], y = res[[i]])
rtime_all[[i]] <- adj_fun(rtime_all[[i]])
## Adjust rtime < smallest adjusted rtime.
if (length(idx_below)) {
rtime_all[[i]][idx_below] <- vals_below +
res[[i]][1] - rtime_sub[[i]][1]
}
## Adjust rtime > largest adjusted rtime
if (length(idx_above)) {
rtime_all[[i]][idx_above] <- vals_above +
res[[i]][n_vals] - rtime_sub[[i]][n_vals]
}
}
res <- rtime_all
}
res <- unlist(res, use.names = FALSE)
sNames <- unlist(split(featureNames(object),
as.factor(fromFile(object))),
use.names = FALSE)
names(res) <- sNames
res <- res[featureNames(object)]
res
})
#' @rdname extractMsData-method
setMethod("extractMsData", signature(object = "OnDiskMSnExp"),
function(object, rt, mz, msLevel = 1L) {
.Deprecated(msg = paste0("Use of 'extractMsData' is deprecated.",
" Please use 'as(x, \"data.frame\")'"))
.extractMsData(object, rt = rt, mz = mz, msLevel = msLevel)
})
setMethod("hasAdjustedRtime", signature(object = "OnDiskMSnExp"),
function(object)
FALSE
)
#' @title Extract isolation window target m/z definition
#'
#' @aliases isolationWindowTargetMz
#'
#' @description
#'
#' `isolationWindowTargetMz` extracts the isolation window target m/z definition
#' for each spectrum in `object`.
#'
#' @param object [OnDiskMSnExp-class] object.
#'
#' @return a `numeric` of length equal to the number of spectra in `object` with
#' the isolation window target m/z or `NA` if not specified/available.
#'
#' @author Johannes Rainer
#'
#' @md
setMethod("isolationWindowTargetMz", "OnDiskMSnExp", function(object) {
if ("isolationWindowTargetMZ" %in% colnames(fData(object)))
return(fData(object)$isolationWindowTargetMZ)
rep(NA_real_, length(object))
})
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Defines functions .peaks_to_result
## Methods for MSnbase's OnDiskMSnExp and MSnExp objects.
#' @include DataClasses.R functions-OnDiskMSnExp.R do_findChromPeaks-functions.R
## Main roxygen documentation for the centWace feature detection is in
## DataClasses, before the definition of the CentWaveParam class.
## The centWave peak detection method for OnDiskMSnExp:
#' @title Chromatographic peak detection using the centWave method
#'
#' @description The \code{detectChromPeaks,OnDiskMSnExp,CentWaveParam} method
#' performs chromatographic peak detection using the \emph{centWave}
#' algorithm on all samples from an \code{\link{OnDiskMSnExp}}
#' object. \code{\link{OnDiskMSnExp}} objects encapsule all
#' experiment specific data and load the spectra data (mz and intensity
#' values) on the fly from the original files applying also all eventual
#' data manipulations.
#'
#' @details Parallel processing (one process per sample) is supported and can
#' be configured either by the \code{BPPARAM} parameter or by globally
#' defining the parallel processing mode using the
#' \code{\link{register}} method from the \code{BiocParallel}
#' package.
#'
#' @param object For \code{findChromPeaks}: an
#' \code{\link{OnDiskMSnExp}} object containing the MS- and all
#' other experiment-relevant data.
#'
#' For all other methods: a parameter object.
#'
#' @param param An \code{CentWaveParam} object containing all settings for the
#' centWave algorithm.
#'
#' @param BPPARAM A parameter class specifying if and how parallel processing
#' should be performed. It defaults to \code{\link{bpparam}}.
#' See documentation of the \code{BiocParallel} for more details. If
#' parallel processing is enabled, peak detection is performed in parallel
#' on several of the input samples.
#'
#' @param return.type Character specifying what type of object the method should
#' return. Can be either \code{"XCMSnExp"} (default), \code{"list"} or
#' \code{"xcmsSet"}.
#'
#' @param msLevel \code{integer(1)} defining the MS level on which the peak
#' detection should be performed. Defaults to \code{msLevel = 1}.
#'
#' @return For \code{findChromPeaks}: if \code{return.type = "XCMSnExp"} an
#' \code{\link{XCMSnExp}} object with the results of the peak detection.
#' If \code{return.type = "list"} a list of length equal to the number of
#' samples with matrices specifying the identified peaks.
#' If \code{return.type = "xcmsSet"} an \code{\linkS4class{xcmsSet}} object
#' with the results of the peak detection.
#'
#' @seealso \code{\link{XCMSnExp}} for the object containing the results of
#' the peak detection.
#'
#' @rdname findChromPeaks-centWave
setMethod("findChromPeaks",
signature(object = "OnDiskMSnExp", param = "CentWaveParam"),
function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
msLevel = 1L) {
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported", call. = FALSE)
## Check if the data is centroided
centroided <- all(centroided(object)[msLevel(object) %in% msLevel])
if (is.na(centroided)) {
idx <- which(msLevel(object) %in% msLevel)
idx <- idx[ceiling(length(idx) / 3)]
suppressWarnings(
centroided <- isCentroided(object[[idx]])
)
}
if (is.na(centroided) || !centroided)
warning("Your data appears to be not centroided! CentWave",
" works best on data in centroid mode.")
resList <- bplapply(.split_by_file2(object, msLevel. = msLevel),
FUN = findChromPeaks_OnDiskMSnExp,
method = "centWave",
param = param, BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
fnames = fileNames(object))
if (return.type == "list")
return(res$peaks)
object <- .peaks_to_result(res, object, startDate, param, msLevel)
if (return.type == "xcmsSet")
as(object, "xcmsSet")
else object
})
## The matchedFilter peak detection method for OnDiskMSnExp:
#' @title Peak detection in the chromatographic time domain
#'
#' @description The \code{findChromPeaks,OnDiskMSnExp,MatchedFilterParam}
#' method performs peak detection using the \emph{matchedFilter} algorithm
#' on all samples from an \code{\link{OnDiskMSnExp}} object.
#' \code{\link{OnDiskMSnExp}} objects encapsule all experiment
#' specific data and load the spectra data (mz and intensity values) on the
#' fly from the original files applying also all eventual data
#' manipulations.
#'
#' @details Parallel processing (one process per sample) is supported and can
#' be configured either by the \code{BPPARAM} parameter or by globally
#' defining the parallel processing mode using the
#' \code{\link{register}} method from the \code{BiocParallel}
#' package.
#'
#' @param object For \code{findChromPeaks}: an
#' \code{\link{OnDiskMSnExp}} object containing the MS- and all
#' other experiment-relevant data.
#'
#' For all other methods: a parameter object.
#'
#' @param param An \code{MatchedFilterParam} object containing all settings for
#' the matchedFilter algorithm.
#'
#' @inheritParams findChromPeaks-centWave
#'
#' @return For \code{findChromPeaks}: if \code{return.type = "XCMSnExp"} an
#' \code{\link{XCMSnExp}} object with the results of the peak detection.
#' If \code{return.type = "list"} a list of length equal to the number of
#' samples with matrices specifying the identified peaks.
#' If \code{return.type = "xcmsSet"} an \code{\linkS4class{xcmsSet}} object
#' with the results of the peak detection.
#'
#' @seealso \code{\link{XCMSnExp}} for the object containing the results of
#' the chromatographic peak detection.
#'
#' @rdname findChromPeaks-matchedFilter
setMethod("findChromPeaks",
signature(object = "OnDiskMSnExp", param = "MatchedFilterParam"),
function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
msLevel = 1L) {
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported")
resList <- bplapply(.split_by_file2(object, msLevel. = msLevel),
FUN = findChromPeaks_OnDiskMSnExp,
method = "matchedFilter",
param = param,
BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
fnames = fileNames(object))
if (return.type == "list")
return(res$peaks)
object <- .peaks_to_result(res, object, startDate, param, msLevel)
if (return.type == "xcmsSet")
as(object, "xcmsSet")
else object
})
#' Simple helper function to convert the peak finding results to an XCMSnExp
#' result object.
#'
#' @noRd
.peaks_to_result <- function(res, object, startDate, param, msLevel) {
xph <- XProcessHistory(param = param, date. = startDate,
type. = .PROCSTEP.PEAK.DETECTION,
fileIndex = 1:length(fileNames(object)),
msLevel = msLevel)
object <- as(object, "XCMSnExp")
phist <- object@.processHistory
## if (hasAdjustedRtime(object) | hasFeatures(object))
## object@msFeatureData <- new("MsFeatureData")
pks <- do.call(rbind, res$peaks)
if (length(pks) > 0) {
chromPeaks(object) <- pks
chromPeakData(object)$ms_level <- as.integer(msLevel)
chromPeakData(object)$is_filled <- FALSE
}
object@.processHistory <- c(phist, list(xph))
validObject(object)
object
}
## massifquant
## The massifquant peak detection method for OnDiskMSnExp:
#' @title Chromatographic peak detection using the massifquant method
#'
#' @description The \code{findChromPeaks,OnDiskMSnExp,MassifquantParam}
#' method performs chromatographic peak detection using the
#' \emph{massifquant} algorithm on all samples from an
#' \code{\link{OnDiskMSnExp}} object.
#' \code{\link{OnDiskMSnExp}} objects encapsule all experiment
#' specific data and load the spectra data (mz and intensity values) on the
#' fly from the original files applying also all eventual data
#' manipulations.
#'
#' @details Parallel processing (one process per sample) is supported and can
#' be configured either by the \code{BPPARAM} parameter or by globally
#' defining the parallel processing mode using the
#' \code{\link{register}} method from the \code{BiocParallel}
#' package.
#'
#' @param object For \code{findChromPeaks}: an
#' \code{\link{OnDiskMSnExp}} object containing the MS- and all
#' other experiment-relevant data.
#'
#' For all other methods: a parameter object.
#'
#' @param param An \code{MassifquantParam} object containing all settings for
#' the massifquant algorithm.
#'
#' @inheritParams findChromPeaks-centWave
#'
#' @return For \code{findChromPeaks}: if \code{return.type = "XCMSnExp"} an
#' \code{\link{XCMSnExp}} object with the results of the peak detection.
#' If \code{return.type = "list"} a list of length equal to the number of
#' samples with matrices specifying the identified peaks.
#' If \code{return.type = "xcmsSet"} an \code{\linkS4class{xcmsSet}} object
#' with the results of the peak detection.
#'
#' @seealso \code{\link{XCMSnExp}} for the object containing the results of
#' the peak detection.
#'
#' @rdname findChromPeaks-massifquant
setMethod("findChromPeaks",
signature(object = "OnDiskMSnExp", param = "MassifquantParam"),
function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
msLevel = 1L) {
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported")
resList <- bplapply(.split_by_file2(object, msLevel. = msLevel),
FUN = findChromPeaks_OnDiskMSnExp,
method = "massifquant", param = param,
BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
fnames = fileNames(object))
if (return.type == "list")
return(res$peaks)
object <- .peaks_to_result(res, object, startDate, param, msLevel)
if (return.type == "xcmsSet")
as(object, "xcmsSet")
else object
})
## MSW
## The MSW peak detection method for OnDiskMSnExp:
#' @title Single-spectrum non-chromatography MS data peak detection
#'
#' @description The \code{findChromPeaks,OnDiskMSnExp,MSWParam}
#' method performs peak detection in single-spectrum non-chromatography MS
#' data using functionality from the \code{MassSpecWavelet} package on all
#' samples from an \code{\link{OnDiskMSnExp}} object.
#' \code{\link{OnDiskMSnExp}} objects encapsule all experiment
#' specific data and load the spectra data (mz and intensity values) on the
#' fly from the original files applying also all eventual data
#' manipulations.
#'
#' @details Parallel processing (one process per sample) is supported and can
#' be configured either by the \code{BPPARAM} parameter or by globally
#' defining the parallel processing mode using the
#' \code{\link{register}} method from the \code{BiocParallel}
#' package.
#'
#' @param object For \code{findChromPeaks}: an
#' \code{\link{OnDiskMSnExp}} object containing the MS- and all
#' other experiment-relevant data.
#'
#' For all other methods: a parameter object.
#'
#' @param param An \code{MSWParam} object containing all settings for
#' the algorithm.
#'
#' @inheritParams findChromPeaks-centWave
#'
#' @return For \code{findChromPeaks}: if \code{return.type = "XCMSnExp"} an
#' \code{\link{XCMSnExp}} object with the results of the peak detection.
#' If \code{return.type = "list"} a list of length equal to the number of
#' samples with matrices specifying the identified peaks.
#' If \code{return.type = "xcmsSet"} an \code{\linkS4class{xcmsSet}} object
#' with the results of the detection.
#'
#' @seealso \code{\link{XCMSnExp}} for the object containing the results of
#' the peak detection.
#'
#' @rdname findPeaks-MSW
setMethod("findChromPeaks",
signature(object = "OnDiskMSnExp", param = "MSWParam"),
function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
msLevel = 1L) {
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported")
object_mslevel <- filterMsLevel(object, msLevel. = msLevel)
if (length(object_mslevel) == 0)
stop("No MS level ", msLevel, " spectra present to perform ",
"peak detection")
rts <- split(rtime(object_mslevel),
f = as.factor(fromFile(object_mslevel)))
if (any(lengths(rts) > 1))
stop("The MSW method can only be applied to single spectrum,",
" non-chromatographic, files (i.e. with a single ",
"retention time).")
resList <- bplapply(.split_by_file2(object_mslevel),
FUN = findPeaks_MSW_OnDiskMSnExp,
method = "MSW", param = param,
BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
fnames = fileNames(object_mslevel))
if (return.type == "list")
return(res$peaks)
object <- .peaks_to_result(res, object, startDate, param, msLevel)
if (return.type == "xcmsSet")
as(object, "xcmsSet")
else object
})
## The centWave with predicted isotope peak detection method for OnDiskMSnExp:
#' @title Two-step centWave peak detection considering also isotopes
#'
#' @description The \code{findChromPeaks,OnDiskMSnExp,CentWavePredIsoParam}
#' method performs a two-step centWave-based chromatographic peak detection
#' on all samples from an \code{\link{OnDiskMSnExp}} object.
#' \code{\link{OnDiskMSnExp}} objects encapsule all experiment
#' specific data and load the spectra data (mz and intensity values) on the
#' fly from the original files applying also all eventual data
#' manipulations.
#'
#' @details Parallel processing (one process per sample) is supported and can
#' be configured either by the \code{BPPARAM} parameter or by globally
#' defining the parallel processing mode using the
#' \code{\link{register}} method from the \code{BiocParallel}
#' package.
#'
#' @param param An \code{CentWavePredIsoParam} object with the settings for the
#' chromatographic peak detection algorithm.
#'
#' @inheritParams findChromPeaks-centWave
#'
#' @return For \code{findChromPeaks}: if \code{return.type = "XCMSnExp"} an
#' \code{\link{XCMSnExp}} object with the results of the peak detection.
#' If \code{return.type = "list"} a list of length equal to the number of
#' samples with matrices specifying the identified peaks.
#' If \code{return.type = "xcmsSet"} an \code{\linkS4class{xcmsSet}} object
#' with the results of the peak detection.
#'
#' @seealso \code{\link{XCMSnExp}} for the object containing the results of
#' the peak detection.
#'
#' @rdname findChromPeaks-centWaveWithPredIsoROIs
setMethod("findChromPeaks",
signature(object = "OnDiskMSnExp", param = "CentWavePredIsoParam"),
function(object, param, BPPARAM = bpparam(), return.type = "XCMSnExp",
msLevel = 1L) {
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported")
## Check if the data is centroided
centroided <- all(centroided(object)[msLevel(object) %in% msLevel])
if (is.na(centroided)) {
idx <- which(msLevel(object) %in% msLevel)
idx <- idx[ceiling(length(idx) / 3)]
suppressWarnings(
centroided <- isCentroided(object[[idx]])
)
}
if (is.na(centroided) || !centroided)
warning("Your data appears to be not centroided! CentWave",
" works best on data in centroid mode.")
resList <- bplapply(.split_by_file2(object, msLevel. = msLevel),
FUN = findChromPeaks_OnDiskMSnExp,
method = "centWaveWithPredIsoROIs",
param = param, BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
fnames = fileNames(object))
if (return.type == "list")
return(res$peaks)
object <- .peaks_to_result(res, object, startDate, param, msLevel)
if (return.type == "xcmsSet")
as(object, "xcmsSet")
else object
})
## profMat method for XCMSnExp/OnDiskMSnExp.
#' @description \code{profMat}: creates a \emph{profile matrix}, which
#' is a n x m matrix, n (rows) representing equally spaced m/z values (bins)
#' and m (columns) the retention time of the corresponding scans. Each cell
#' contains the maximum intensity measured for the specific scan and m/z
#' values. See \code{\link{profMat}} for more details and description of
#' the various binning methods.
#'
#' @param ... Additional parameters.
#'
#' @return For \code{profMat}: a \code{list} with a the profile matrix
#' \code{matrix} (or matrices if \code{fileIndex} was not specified or if
#' \code{length(fileIndex) > 1}). See \code{\link{profile-matrix}} for
#' general help and information about the profile matrix.
#'
#' @inheritParams profMat-xcmsSet
#'
#' @rdname XCMSnExp-class
setMethod("profMat", signature(object = "OnDiskMSnExp"), function(object,
method = "bin",
step = 0.1,
baselevel = NULL,
basespace = NULL,
mzrange. = NULL,
fileIndex,
...) {
## Subset the object by fileIndex.
if (!missing(fileIndex)) {
if (!is.numeric(fileIndex))
stop("'fileIndex' has to be an integer.")
if (!all(fileIndex %in% seq_along(fileNames(object))))
stop("'fileIndex' has to be an integer between 1 and ",
length(fileNames(object)), "!")
object <- filterFile(object, fileIndex)
}
## Split it by file and bplapply over it to generate the profile matrix.
theF <- factor(seq_along(fileNames(object)))
theDots <- list(...)
if (any(names(theDots) == "returnBreaks"))
returnBreaks <- theDots$returnBreaks
else
returnBreaks <- FALSE
res <- bplapply(splitByFile(object, f = theF), function(z, bmethod, bstep,
bbaselevel,
bbasespace,
bmzrange.,
breturnBreaks) {
require(xcms, quietly = TRUE)
sps <- spectra(z, BPPARAM = SerialParam())
mzs <- lapply(sps, mz)
## Fix for issue #301: got spectra with m/z being NA.
if (any(is.na(unlist(mzs, use.names = FALSE)))) {
sps <- lapply(sps, clean, all = TRUE)
mzs <- lapply(sps, mz)
}
## Fix for issue #312: remove empty spectra, that we are however adding
## later so that the ncol(profMat) == length(rtime(object))
pk_count <- lengths(mzs)
empty_spectra <- which(pk_count == 0)
if (length(empty_spectra)) {
mzs <- mzs[-empty_spectra]
sps <- sps[-empty_spectra]
}
vps <- lengths(mzs, use.names = FALSE)
res <- .createProfileMatrix(mz = unlist(mzs, use.names = FALSE),
int = unlist(lapply(sps, intensity),
use.names = FALSE),
valsPerSpect = vps,
method = bmethod,
step = bstep,
baselevel = bbaselevel,
basespace = bbasespace,
mzrange. = bmzrange.,
returnBreaks = breturnBreaks)
if (length(empty_spectra))
if (returnBreaks)
res$profMat <- .insertColumn(res$profMat, empty_spectra, 0)
else
res <- .insertColumn(res, empty_spectra, 0)
res
}, bmethod = method, bstep = step, bbaselevel = baselevel,
bbasespace = basespace, bmzrange. = mzrange., breturnBreaks = returnBreaks)
res
})
#' @rdname adjustRtime-obiwarp
setMethod("adjustRtime",
signature(object = "OnDiskMSnExp", param = "ObiwarpParam"),
function(object, param, msLevel = 1L) {
## Filter for MS level, perform adjustment and if the object
## contains spectra from other MS levels too, adjust all raw
## rts based on the difference between adjusted and raw rts.
object_sub <- filterMsLevel(object, msLevel = msLevel)
if (length(object_sub) == 0)
stop("No spectra of MS level ", msLevel, " present")
res <- .obiwarp(object_sub, param = param)
## Adjust the retention time for spectra of all MS levels, if
## if there are some other than msLevel (issue #214).
if (length(unique(msLevel(object))) !=
length(unique(msLevel(object_sub)))) {
message("Apply retention time correction performed on MS",
msLevel, " to spectra from all MS levels")
## I need raw and adjusted rt for the adjusted spectra
## and the raw rt of all.
rtime_all <- split(rtime(object), fromFile(object))
rtime_sub <- split(rtime(object_sub), fromFile(object_sub))
## For loop is faster than lapply. No sense to do parallel
for (i in 1:length(rtime_all)) {
n_vals <- length(rtime_sub[[i]])
idx_below <- which(rtime_all[[i]] < rtime_sub[[i]][1])
if (length(idx_below))
vals_below <- rtime_all[[i]][idx_below]
idx_above <- which(rtime_all[[i]] >
rtime_sub[[i]][n_vals])
if (length(idx_above))
vals_above <- rtime_all[[i]][idx_above]
## Adjust the retention time. Note: this should be
## OK even if values are not sorted.
adj_fun <- approxfun(x = rtime_sub[[i]], y = res[[i]])
rtime_all[[i]] <- adj_fun(rtime_all[[i]])
## Adjust rtime < smallest adjusted rtime.
if (length(idx_below)) {
rtime_all[[i]][idx_below] <- vals_below +
res[[i]][1] - rtime_sub[[i]][1]
}
## Adjust rtime > largest adjusted rtime
if (length(idx_above)) {
rtime_all[[i]][idx_above] <- vals_above +
res[[i]][n_vals] - rtime_sub[[i]][n_vals]
}
}
res <- rtime_all
}
res <- unlist(res, use.names = FALSE)
sNames <- unlist(split(featureNames(object),
as.factor(fromFile(object))),
use.names = FALSE)
names(res) <- sNames
res <- res[featureNames(object)]
res
})
#' @rdname extractMsData-method
setMethod("extractMsData", signature(object = "OnDiskMSnExp"),
function(object, rt, mz, msLevel = 1L) {
.Deprecated(msg = paste0("Use of 'extractMsData' is deprecated.",
" Please use 'as(x, \"data.frame\")'"))
.extractMsData(object, rt = rt, mz = mz, msLevel = msLevel)
})
setMethod("hasAdjustedRtime", signature(object = "OnDiskMSnExp"),
function(object)
FALSE
)
#' @title Extract isolation window target m/z definition
#'
#' @aliases isolationWindowTargetMz
#'
#' @description
#'
#' `isolationWindowTargetMz` extracts the isolation window target m/z definition
#' for each spectrum in `object`.
#'
#' @param object [OnDiskMSnExp-class] object.
#'
#' @return a `numeric` of length equal to the number of spectra in `object` with
#' the isolation window target m/z or `NA` if not specified/available.
#'
#' @author Johannes Rainer
#'
#' @md
setMethod("isolationWindowTargetMz", "OnDiskMSnExp", function(object) {
if ("isolationWindowTargetMZ" %in% colnames(fData(object)))
return(fData(object)$isolationWindowTargetMZ)
rep(NA_real_, length(object))
})
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