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findChromPeaks,XCMSnExp uses adjusted retention time if present
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- findChromPeaks,XCMSnExp uses adjusted retention times if present (issues #208,
  #213.
- Add respective unit tests.
- New parameter msLevel for processHistory,XCMSnExp.
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@jorainer
jorainer committed Aug 30, 2017
1 parent d9d5812 commit b17a3b3
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Showing 9 changed files with 346 additions and 155 deletions.
11 changes: 7 additions & 4 deletions R/DataClasses.R
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Original file line number Diff line number Diff line change
Expand Up @@ -2218,11 +2218,14 @@ setClass("MsFeatureData", contains = c("environment", "Versioned"),
#' (a \code{DataFrame}) and \code{"adjustedRtime"} (a \code{list} of
#' numeric vectors). Note that these should not be accessed directly but
#' rather \emph{via} their accessor methods.
#'
#' Along with the results, the object contains the processing history that
#' allow to track each processing step along with the used settings. The
#' object also directly extends the \code{\link[MSnbase]{OnDiskMSnExp}}
#' object hence allowing easy access to the full data on which the peak
#' detection was performed.
#' allows to track each processing step along with the used settings. This
#' can be extracted with the \code{\link{processHistory}} method.
#'
#' The \code{XCMSnExp} object directly extends the
#' \code{\link[MSnbase]{OnDiskMSnExp}} object and provides thus an easy
#' access to the full raw data at any stage of an analysis.
#'
#' Objects from this class should not be created directly, they are
#' returned as result from the \code{\link{findChromPeaks}} method.
Expand Down
136 changes: 91 additions & 45 deletions R/methods-OnDiskMSnExp.R
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Original file line number Diff line number Diff line change
Expand Up @@ -71,7 +71,9 @@ setMethod("findChromPeaks",
stop("No MS level ", msLevel, " spectra present to perform ",
"peak detection")
## Check if the data is centroided
centroided <- isCentroided(object[[1]])
suppressWarnings(
centroided <- isCentroided(object[[1]])
)
## issue #181: if there are too few mass peaks the function
## returns NA.
if (is.na(centroided)) {
Expand All @@ -84,13 +86,17 @@ setMethod("findChromPeaks",
if (!centroided)
warning("Your data appears to be not centroided! CentWave",
" works best on data in centroid mode.")
## (1) split the object per file.
## (1) split the object per file. Ensure we keep adjusted
## retention times (issue #213).
args <- list(X = 1:length(fileNames(object)), FUN = filterFile,
object = object)
if (hasAdjustedRtime(object))
args$keepAdjustedRtime <- TRUE
## (2) use bplapply to do the peak detection.
resList <- bplapply(lapply(1:length(fileNames(object)),
filterFile, object = object),
FUN = findChromPeaks_OnDiskMSnExp,
method = "centWave", param = param,
BPPARAM = BPPARAM)
resList <- bplapply(do.call("lapply", args),
FUN = findChromPeaks_OnDiskMSnExp,
method = "centWave",
param = param, BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
Expand All @@ -104,7 +110,7 @@ setMethod("findChromPeaks",
fileIndex = 1:length(fileNames(object)),
msLevel = msLevel)
object <- as(object, "XCMSnExp")
object@.processHistory <- list(xph)
object@.processHistory <- c(processHistory(object), list(xph))
## Support keeping adjusted retention times (issue #210)
## if (hasAdjustedRtime(object) | hasFeatures(object))
## object@msFeatureData <- new("MsFeatureData")
Expand Down Expand Up @@ -235,18 +241,26 @@ setMethod("findChromPeaks",
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS x data.
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported")
object <- filterMsLevel(object, msLevel. = msLevel)
if (length(object) == 0)
stop("No MS level ", msLevel, " spectra present to perform ",
"peak detection")
## (1) split the object per file.
## (1) split the object per file. Ensure we keep adjusted
## retention times (issue #213).
args <- list(X = 1:length(fileNames(object)), FUN = filterFile,
object = object)
if (hasAdjustedRtime(object))
args$keepAdjustedRtime <- TRUE
## (2) use bplapply to do the peak detection.
resList <- bplapply(lapply(1:length(fileNames(object)),
filterFile, object = object),
FUN = findChromPeaks_OnDiskMSnExp,
method = "matchedFilter", param = param,
BPPARAM = BPPARAM)
resList <- bplapply(do.call("lapply", args),
FUN = findChromPeaks_OnDiskMSnExp,
method = "matchedFilter",
param = param,
BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
Expand All @@ -257,9 +271,10 @@ setMethod("findChromPeaks",
## since we're calling the method once on all.
xph <- XProcessHistory(param = param, date. = startDate,
type. = .PROCSTEP.PEAK.DETECTION,
fileIndex = 1:length(fileNames(object)))
fileIndex = 1:length(fileNames(object)),
msLevel = msLevel)
object <- as(object, "XCMSnExp")
object@.processHistory <- list(xph)
object@.processHistory <- c(processHistory(object), list(xph))
if (hasAdjustedRtime(object) | hasFeatures(object))
object@msFeatureData <- new("MsFeatureData")
pks <- do.call(rbind, res$peaks)
Expand Down Expand Up @@ -380,18 +395,25 @@ setMethod("findChromPeaks",
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS x data.
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported")
object <- filterMsLevel(object, msLevel. = msLevel)
if (length(object) == 0)
stop("No MS level ", msLevel, " spectra present to perform ",
"peak detection")
## (1) split the object per file.
## (1) split the object per file. Ensure we keep adjusted
## retention times (issue #213).
args <- list(X = 1:length(fileNames(object)), FUN = filterFile,
object = object)
if (hasAdjustedRtime(object))
args$keepAdjustedRtime <- TRUE
## (2) use bplapply to do the peaks detection.
resList <- bplapply(lapply(1:length(fileNames(object)),
filterFile, object = object),
FUN = findChromPeaks_OnDiskMSnExp,
method = "massifquant", param = param,
BPPARAM = BPPARAM)
resList <- bplapply(do.call("lapply", args),
FUN = findChromPeaks_OnDiskMSnExp,
method = "massifquant", param = param,
BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
Expand All @@ -402,9 +424,10 @@ setMethod("findChromPeaks",
## since we're calling the method once on all.
xph <- XProcessHistory(param = param, date. = startDate,
type. = .PROCSTEP.PEAK.DETECTION,
fileIndex = 1:length(fileNames(object)))
fileIndex = 1:length(fileNames(object)),
msLevel = msLevel)
object <- as(object, "XCMSnExp")
object@.processHistory <- list(xph)
object@.processHistory <- c(processHistory(object), list(xph))
if (hasAdjustedRtime(object) | hasFeatures(object))
object@msFeatureData <- new("MsFeatureData")
pks <- do.call(rbind, res$peaks)
Expand Down Expand Up @@ -527,7 +550,10 @@ setMethod("findChromPeaks",
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS x data.
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported")
object <- filterMsLevel(object, msLevel. = msLevel)
if (length(object) == 0)
stop("No MS level ", msLevel, " spectra present to perform ",
Expand All @@ -538,13 +564,17 @@ setMethod("findChromPeaks",
stop("The MSW method can only be applied to single spectrum,",
" non-chromatogrphic, files (i.e. with a single ",
"retention time).")
## (1) split the object per file.
## (1) split the object per file. Ensure we keep adjusted
## retention times (issue #213).
args <- list(X = 1:length(fileNames(object)), FUN = filterFile,
object = object)
if (hasAdjustedRtime(object))
args$keepAdjustedRtime <- TRUE
## (2) use bplapply to do the peak detection.
resList <- bplapply(lapply(1:length(fileNames(object)),
filterFile, object = object),
FUN = findPeaks_MSW_OnDiskMSnExp,
method = "MSW", param = param,
BPPARAM = BPPARAM)
resList <- bplapply(do.call("lapply", args),
FUN = findPeaks_MSW_OnDiskMSnExp,
method = "MSW", param = param,
BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
Expand All @@ -555,9 +585,10 @@ setMethod("findChromPeaks",
## since we're calling the method once on all.
xph <- XProcessHistory(param = param, date. = startDate,
type. = .PROCSTEP.PEAK.DETECTION,
fileIndex = 1:length(fileNames(object)))
fileIndex = 1:length(fileNames(object)),
msLevel = msLevel)
object <- as(object, "XCMSnExp")
object@.processHistory <- list(xph)
object@.processHistory <- c(processHistory(object), list(xph))
if (hasAdjustedRtime(object) | hasFeatures(object))
object@msFeatureData <- new("MsFeatureData")
pks <- do.call(rbind, res$peaks)
Expand Down Expand Up @@ -671,13 +702,18 @@ setMethod("findChromPeaks",
return.type <- match.arg(return.type, c("XCMSnExp", "list",
"xcmsSet"))
startDate <- date()
## Restrict to MS x data.
## Restrict to MS X data.
if (length(msLevel) > 1)
stop("Currently only peak detection in a single MS level is ",
"supported")
object <- filterMsLevel(object, msLevel. = msLevel)
if (length(object) == 0)
stop("No MS level ", msLevel, " spectra present to perform ",
"peak detection")
## Check if the data is centroided
centroided <- isCentroided(object[[1]])
suppressWarnings(
centroided <- isCentroided(object[[1]])
)
## issue #181: if there are too few mass peaks the function
## returns NA.
if (is.na(centroided)) {
Expand All @@ -690,13 +726,17 @@ setMethod("findChromPeaks",
if (!centroided)
warning("Your data appears to be not centroided! CentWave",
" works best on data in centroid mode.")
## (1) split the object per file.
## (1) split the object per file. Ensure we keep adjusted
## retention times (issue #213).
args <- list(X = 1:length(fileNames(object)), FUN = filterFile,
object = object)
if (hasAdjustedRtime(object))
args$keepAdjustedRtime <- TRUE
## (2) use bplapply to do the peak detection.
resList <- bplapply(lapply(1:length(fileNames(object)),
filterFile, object = object),
FUN = findChromPeaks_OnDiskMSnExp,
method = "centWaveWithPredIsoROIs", param = param,
BPPARAM = BPPARAM)
resList <- bplapply(do.call("lapply", args),
FUN = findChromPeaks_OnDiskMSnExp,
method = "centWaveWithPredIsoROIs",
param = param, BPPARAM = BPPARAM)
## (3) collect the results.
res <- .processResultList(resList,
getProcHist = return.type == "xcmsSet",
Expand All @@ -707,9 +747,10 @@ setMethod("findChromPeaks",
## since we're calling the method once on all.
xph <- XProcessHistory(param = param, date. = startDate,
type. = .PROCSTEP.PEAK.DETECTION,
fileIndex = 1:length(fileNames(object)))
fileIndex = 1:length(fileNames(object)),
msLevel = msLevel)
object <- as(object, "XCMSnExp")
object@.processHistory <- list(xph)
object@.processHistory <- c(processHistory(object), list(xph))
if (hasAdjustedRtime(object) | hasFeatures(object))
object@msFeatureData <- new("MsFeatureData")
pks <- do.call(rbind, res$peaks)
Expand Down Expand Up @@ -883,3 +924,8 @@ setMethod("extractMsData", signature(object = "OnDiskMSnExp"),
function(object, rt, mz) {
.extractMsData(object, rt = rt, mz = mz)
})

setMethod("hasAdjustedRtime", signature(object = "OnDiskMSnExp"),
function(object)
FALSE
)

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