From 2f74bd5443fa08e4dd039d720d8759a4b41609ee Mon Sep 17 00:00:00 2001
From: Michele Stravs <stravsmi@eawag.ch>
Date: Thu, 4 Dec 2014 11:43:59 +0100
Subject: [PATCH] msmsWorkspace update: specs and analyzedSpecs to spectra
---
R/RmbWorkspace.R | 61 +++++++--
R/RmbWorkspaceUpdate.R | 279 +++++++++++++++++++++++++++++++++++++++++
R/SpectrumClasses.R | 76 ++++++-----
R/SpectrumMethods.R | 2 +-
4 files changed, 378 insertions(+), 40 deletions(-)
create mode 100644 R/RmbWorkspaceUpdate.R
diff --git a/R/RmbWorkspace.R b/R/RmbWorkspace.R
index 48b08dd..402aa12 100755
--- a/R/RmbWorkspace.R
+++ b/R/RmbWorkspace.R
@@ -1,6 +1,9 @@
#' @import methods
NULL
+
+setClassUnion("msmsWorkspaceOrNULL", "NULL")
+
#' Workspace for \code{msmsWorkflow} data
#'
#' A workspace which stores input and output data for \code{\link{msmsWorkflow}}.
@@ -46,7 +49,7 @@ NULL
## ' peaks (after step 7, see \code{\link{reanalyzeFailpeaks}}).
## ' @slot refilteredRcSpecs Final data to use for MassBank record creation after
## ' multiplicity filtering (step 8).
-#'
+##'
## ' @method show,msmsWorkflow Shows a brief summary of the object. Currently only the included files.
#'
#' @seealso \code{\link{msmsWorkflow}}
@@ -55,10 +58,11 @@ NULL
#' @docType class
#' @exportClass msmsWorkspace
#' @export
-setClass("msmsWorkspace",
- representation(
+.msmsWorkspace <- setClass("msmsWorkspace",
+ representation = representation(
files = "character",
- specs = "list",
+ spectra = "RmbSpectraSetList",
+ parent = "msmsWorkspaceOrNULL",
analyzedSpecs = "list",
aggregatedSpecs = "list",
rc = "ANY",
@@ -70,8 +74,39 @@ setClass("msmsWorkspace",
refilteredRcSpecs = "list",
archivename = "character",
settings = "list"
- ),
+ ),
+ contains=c("Versioned"),
+ prototype = prototype(
+ new("Versioned", versions=c(msmsWorkspace = "2.0.1")),
+ parent = NULL
)
+)
+
+setIs("msmsWorkspace", "msmsWorkspaceOrNULL")
+
+#.msmsWorkspace <- setClass("msmsWorkspace",
+# representation = representation(
+# files = "character",
+# specs = "list",
+# analyzedSpecs = "list",
+# aggregatedSpecs = "list",
+# rc = "ANY",
+# rc.ms1 = "ANY",
+# recalibratedSpecs = "list",
+# analyzedRcSpecs = "list",
+# aggregatedRcSpecs = "list",
+# reanalyzedRcSpecs = "list",
+# refilteredRcSpecs = "list",
+# archivename = "character",
+# settings = "list"
+# ),
+# contains=c("Versioned"),
+# prototype = prototype(
+# new("Versioned", versions=c(msmsWorkspace = "1.0.1"))
+# )
+# )
+
+
#' Workspace for \code{mbWorkflow} data
#'
@@ -159,7 +194,7 @@ loadMsmsWorkspace <- function(fileName, loadSettings = FALSE)
load(fileName, envir=tempEnv)
# Look if there is a msmsWorkspace in the file
objs <- ls(tempEnv)
- isWs <- unlist(lapply(objs, function(obj) "msmsWorkspace" %in% class(tempEnv[[obj]])))
+ isWs <- unlist(lapply(objs, function(obj) is(tempEnv[[obj]], "msmsWorkspace")))
whichWs <- match(TRUE, isWs)
# Found? Then just return it.
if(!is.na(whichWs))
@@ -169,7 +204,7 @@ loadMsmsWorkspace <- function(fileName, loadSettings = FALSE)
if(loadSettings == FALSE)
w@settings <- list()
}
- # Otherwise hope to load the dataset into a new workspace
+ # If there is no msmsWorkspace object in the workspace, this means that the workspace is version 1!
else
{
w <- new("msmsWorkspace")
@@ -188,12 +223,22 @@ loadMsmsWorkspace <- function(fileName, loadSettings = FALSE)
for(var in dataset)
{
if(exists(var, envir=tempEnv))
- slot(w, var) <- tempEnv[[var]]
+ slot(w, var, check=FALSE) <- tempEnv[[var]]
+ classVersion(w) <- "1.0.0"
}
# Check if settings exist...
if((loadSettings == TRUE) && exists("RmbSettings", envir=tempEnv))
w@settings <- tempEnv$RmbSettings
}
+ # process version updates
+ updateClass <- FALSE
+ if(!isVersioned(w)) updateClass <- TRUE
+ else if(!all(isCurrent(w))) updateClass <- TRUE
+ if(updateClass)
+ {
+ w <- updateObject(w)
+ }
+
# If loadSettings is set: load the settings into RMassBank
if((loadSettings == TRUE) && (length(w@settings) > 0))
loadRmbSettings(w@settings)
diff --git a/R/RmbWorkspaceUpdate.R b/R/RmbWorkspaceUpdate.R
new file mode 100644
index 0000000..441904f
--- /dev/null
+++ b/R/RmbWorkspaceUpdate.R
@@ -0,0 +1,279 @@
+# TODO: Add comment
+#
+# Author: stravsmi
+###############################################################################
+
+
+.updateObject.RmbWorkspace <- setMethod("updateObject", signature(object="msmsWorkspace"), function(object, ..., verbose = FALSE)
+ {
+ w <- object
+ if(isVersioned(w))
+ if(all(isCurrent(w)))
+ return(w)
+ # get msmsWorkspace version
+ if(!isVersioned(w))
+ v <- "1.0.0"
+ else
+ v <- classVersion(w)["msmsWorkspace"]
+ w.new <- w
+ # gradually step up versions
+ # 2.0.1:
+ # * spectra go from specs, analyzedSpecs or their rc analogs to Spectra
+ # * data pre recalibration get shifted to "parent workspace"
+ if(v < "2.0.1")
+ {
+ w.old <- w.new
+ w.new <- new("msmsWorkspace")
+ w.new@files <- w.old@files
+ # Do we have recalibration done? If so: all data in the WS will be the recalibrated data, the unrecalibrated data will be
+ # moved into a new parent workspace which is referenced
+ progress <- .findProgress.v1(w.old)
+ if(4 %in% progress)
+ {
+ w.parent <- w.old
+ w.parent@recalibratedSpecs <- list()
+ w.parent@analyzedRcSpecs <- list()
+ w.parent@aggregatedRcSpecs <- list()
+ w.parent@reanalyzedRcSpecs <- list()
+ w.parent@refilteredRcSpecs <- list()
+ w.old@specs <- w.old@recalibratedSpecs
+ w.old@analyzedSpecs <- w.old@analyzedRcSpecs
+ w.parent.new <- updateObject(w.parent)
+ w.new@parent <- w.parent.new
+ }
+ w.new@spectra <- .updateObject.spectra(w.old@specs, w.old@analyzedSpecs)
+ }
+
+ return(w.new)
+ })
+
+
+
+.updateObject.spectra <- function(specs, analyzedSpecs)
+{
+ if((length(specs) != length(analyzedSpecs)) && (0 != length(analyzedSpecs) ))
+ stop("updateObject: Could not update object because data is inconsistent. length(analyzedSpecs) != length(specs) or 0")
+ # process info ex specs
+ spectra <- lapply(specs, function(spec){
+ set <- new("RmbSpectraSet")
+ # identifiers and properties
+ set@mz <- spec$mz$mzCenter
+ set@id <- as.integer(spec$id)
+ set@formula <- spec$formula
+ set@found <- as.logical(spec$foundOK)
+ # now parent and child MS
+ # check for parent recalibration column
+ if("mzRecal" %in% colnames(spec$parentPeak))
+ mzcol <- "mzRecal"
+ else
+ mzcol <- "mz"
+ set@parent <- new("Spectrum1",
+ mz = spec$parentPeak[,mzcol],
+ intensity = spec$parentPeak[,2],
+ polarity = as.integer(spec$parentHeader$polarity),
+ peaksCount = as.integer(spec$parentHeader$peaksCount),
+ rt = spec$parentHeader$retentionTime,
+ acquisitionNum = as.integer(spec$parentHeader$acquisitionNum),
+ tic = spec$parentHeader$totIonCurrent,
+ centroided = TRUE
+ )
+ # get MSMS data from spec$peaks into RmbSpectrum2 objects
+ children.p1 <- lapply(spec$peaks, function(peaks)
+ {
+ if("mzRecal" %in% colnames(peaks))
+ mzcol <- "mzRecal"
+ else
+ mzcol <- "mz"
+ new("RmbSpectrum2",
+ mz=peaks[,mzcol],
+ intensity=peaks[,2],
+ peaksCount=nrow(peaks))
+ })
+ # get header data from spec$childHeaders into separate RmbSpectrum2 objects
+ children.p2 <- apply(spec$childHeaders, 1, function(line)
+ {
+ new("RmbSpectrum2",
+ precScanNum = as.integer(line["precursorScanNum"]),
+ precursorMz = line["precursorMZ"],
+ precursorIntensity = line["precursorIntensity"],
+ precursorCharge = as.integer(line["precursorCharge"]),
+ collisionEnergy = line["collisionEnergy"],
+ tic = line["totIonCurrent"],
+ rt = line["retentionTime"],
+ acquisitionNum = as.integer(line["acquisitionNum"]),
+ centroided = TRUE
+ )
+ })
+ # merge MSMS RmbSpectrum2 with header RmbSpectrum2
+ children <- mapply(function(c1,c2)
+ {
+ c2slots <- c("precScanNum","precursorMz", "precursorIntensity", "precursorCharge", "collisionEnergy",
+ "tic", "rt", "acquisitionNum", "centroided")
+ for(c2slot in c2slots)
+ slot(c1, c2slot) <- slot(c2, c2slot)
+ return(c1)
+ }, children.p1, children.p2)
+ set@children <- as(children, "SimpleList")
+
+ return(set)
+ })
+ spectra <- mapply(function(set, name)
+ {
+ set@name <- name
+ return(set)
+ },
+ spectra, names(specs))
+
+
+ # add info ex analyzedSpecs if present
+ if(length(analyzedSpecs) > 0)
+ {
+ spectra <- mapply(function(set, analyzedSpec)
+ {
+ if(length(analyzedSpec$msmsdata) != length(set@children))
+ stop("updateObject: Could not update object because data is inconsistent. length(analyzedSpec$msmsdata) != length(set@children)")
+ children <- mapply(function(spectrum, msmsrecord)
+ {
+ if(!is.data.frame(msmsrecord$childBad))
+ msmsrecord$childBad <- data.frame()
+ # note: mz/intensity are replaced with the values from the analyzed spectrum,
+ # such as to have a mass multiple times for multiple matched formulas
+
+ # check if the spectrum has recalibrated masses; if yes, use those
+ if("mzRecal" %in% colnames(msmsrecord$childRaw))
+ mzcol <- "mzRecal"
+ else
+ mzcol <- "mz"
+ spectrum@mz <- c(msmsrecord$childFilt$mzFound,
+ msmsrecord$childBad$mzFound,
+ msmsrecord$childUnmatched$mzFound,
+ msmsrecord$childRawLow[,mzcol],
+ msmsrecord$childRawSatellite[,mzcol])
+ spectrum@intensity <- c(msmsrecord$childFilt$int,
+ msmsrecord$childBad$int,
+ msmsrecord$childUnmatched$int,
+ msmsrecord$childRawLow$int,
+ msmsrecord$childRawSatellite$int)
+ spectrum@peaksCount <- length(spectrum@mz)
+
+ spectrum@satellite <- as.logical(c(
+ rep(FALSE,nrow(msmsrecord$childFilt)),
+ rep(FALSE,nrow(msmsrecord$childBad)),
+ rep(FALSE,nrow(msmsrecord$childUnmatched)),
+ rep(FALSE,nrow(msmsrecord$childRawLow)),
+ rep(TRUE,nrow(msmsrecord$childRawSatellite)))
+ )
+
+
+ spectrum@low <- as.logical(c(
+ rep(FALSE,nrow(msmsrecord$childFilt)),
+ rep(FALSE,nrow(msmsrecord$childBad)),
+ rep(FALSE,nrow(msmsrecord$childUnmatched)),
+ rep(TRUE,nrow(msmsrecord$childRawLow)),
+ rep(FALSE,nrow(msmsrecord$childRawSatellite)))
+ )
+
+ spectrum@rawOK <- as.logical(c(
+ rep(TRUE,nrow(msmsrecord$childFilt)),
+ rep(TRUE,nrow(msmsrecord$childBad)),
+ rep(TRUE,nrow(msmsrecord$childUnmatched)),
+ rep(FALSE,nrow(msmsrecord$childRawLow)),
+ rep(FALSE,nrow(msmsrecord$childRawSatellite)))
+ )
+
+ spectrum@good <- as.logical(c(
+ msmsrecord$childFilt$good,
+ msmsrecord$childBad$good,
+ msmsrecord$childUnmatched$good,
+ rep(NA,nrow(msmsrecord$childRawLow)),
+ rep(NA,nrow(msmsrecord$childRawSatellite)))
+ )
+ spectrum@mzCalc <- as.numeric(c(
+ msmsrecord$childFilt$mzCalc,
+ msmsrecord$childBad$mzCalc,
+ msmsrecord$childUnmatched$mzCalc,
+ rep(NA,nrow(msmsrecord$childRawLow)),
+ rep(NA,nrow(msmsrecord$childRawSatellite)))
+ )
+ spectrum@formula <- as.character(c(
+ msmsrecord$childFilt$formula,
+ msmsrecord$childBad$formula,
+ msmsrecord$childUnmatched$formula,
+ rep(NA,nrow(msmsrecord$childRawLow)),
+ rep(NA,nrow(msmsrecord$childRawSatellite)))
+ )
+
+ spectrum@dbe <- as.numeric(c(
+ msmsrecord$childFilt$dbe,
+ msmsrecord$childBad$dbe,
+ msmsrecord$childUnmatched$dbe,
+ rep(NA,nrow(msmsrecord$childRawLow)),
+ rep(NA,nrow(msmsrecord$childRawSatellite)))
+ )
+
+ spectrum@formulaCount <- as.integer(c(
+ msmsrecord$childFilt$formulaCount,
+ msmsrecord$childBad$formulaCount,
+ msmsrecord$childUnmatched$formulaCount,
+ rep(NA,nrow(msmsrecord$childRawLow)),
+ rep(NA,nrow(msmsrecord$childRawSatellite)))
+ )
+
+ spectrum@dppm <- as.numeric(c(
+ msmsrecord$childFilt$dppm,
+ msmsrecord$childBad$dppm,
+ msmsrecord$childUnmatched$dppm,
+ rep(NA,nrow(msmsrecord$childRawLow)),
+ rep(NA,nrow(msmsrecord$childRawSatellite)))
+ )
+ spectrum@dppmBest <- as.numeric(c(
+ msmsrecord$childFilt$dppmBest,
+ msmsrecord$childBad$dppmBest,
+ msmsrecord$childUnmatched$dppmBest,
+ rep(NA,nrow(msmsrecord$childRawLow)),
+ rep(NA,nrow(msmsrecord$childRawSatellite)))
+ )
+
+# .RmbSpectrum2 <- setClass("RmbSpectrum2",
+# representation = representation(
+ ## satellite="logical",
+ ## low="logical",
+ ## rawOK ="logical",
+ ## good = "logical",
+ ## mzCalc = "numeric",
+ ## formula = "character",
+ ## formulaCount = "integer",
+ ## dppm = "numeric",
+ ## dppmBest = "numeric",
+# ),
+
+ return(spectrum)
+
+ },
+ set@children, analyzedSpec$msmsdata)
+ set@children <- as(children, "SimpleList")
+ return(set)
+ },
+ spectra, analyzedSpecs)
+ }
+
+
+ return(as(spectra, "SimpleList"))
+
+}
+
+# Finds progress in the "old workspace version" to determine whether to take the old spectra or the recalibrated ones (and
+# make a parent workspace)
+.findProgress.v1 <- function(workspace)
+{
+ step1 <- (length(workspace@specs) > 0)
+ step2 <- (length(workspace@analyzedSpecs) > 0)
+ step3 <- (length(workspace@aggregatedSpecs) > 0)
+ step4 <- (length(workspace@recalibratedSpecs) > 0)
+ step5 <- (length(workspace@analyzedRcSpecs) > 0)
+ step6 <- (length(workspace@aggregatedRcSpecs) > 0)
+ step7 <- (length(workspace@reanalyzedRcSpecs) > 0)
+ step8 <- (length(workspace@refilteredRcSpecs) > 0)
+ steps <- which(c(step1, step2, step3, step4, step5, step6, step7, step8))
+ return(steps)
+}
\ No newline at end of file
diff --git a/R/SpectrumClasses.R b/R/SpectrumClasses.R
index c1b88e4..2205543 100644
--- a/R/SpectrumClasses.R
+++ b/R/SpectrumClasses.R
@@ -1,7 +1,44 @@
-setClass("RmbSpectraSet",
+.RmbSpectrum2 <- setClass("RmbSpectrum2",
+ representation = representation(
+ satellite="logical",
+ low="logical",
+ rawOK ="logical",
+ good = "logical",
+ mzCalc = "numeric",
+ formula = "character",
+ dbe = "numeric",
+ formulaCount = "integer",
+ dppm = "numeric",
+ dppmBest = "numeric"
+ ),
+ contains=c("Spectrum2"),
+ prototype = prototype(
+ satellite = logical(),
+ low = logical(),
+ rawOK = logical(),
+ good = logical(),
+ mzCalc = numeric(),
+ formula = character(),
+ dbe = numeric(),
+ formulaCount = integer(),
+ dppm = numeric(),
+ dppmBest = numeric(),
+ new("Versioned", versions=c(classVersion("Spectrum2"), RmbSpectrum2 = "0.1.0"))
+ ),
+)
+
+.RmbSpectrum2List <- setClass("RmbSpectrum2List", contains="SimpleList",
+ prototype=prototype(elementType="RmbSpectrum2"))
+#
+#setAs("ANY", "RmbSpectrum2List", function(from) {
+# coerceToSimpleList(from)
+# })
+
+
+.RmbSpectraSet <- setClass("RmbSpectraSet",
representation = representation(
parent = "Spectrum1",
- children = "list",
+ children = "RmbSpectrum2List",
# These are done as slots and not as S4 functions, because they are set during the workflow
# in "checking" steps. It's easier.
found = "logical",
@@ -15,7 +52,7 @@ setClass("RmbSpectraSet",
),
prototype = prototype(
parent = new("Spectrum1"),
- children = list(),
+ children = new("RmbSpectrum2List"),
found = FALSE,
complete = NA,
empty = NA,
@@ -25,36 +62,13 @@ setClass("RmbSpectraSet",
name = character(),
annotations = list()
)
- ,
- validity = function(object)
- {
- childrenSpectraOK <- all(unlist(lapply(object@children, function(s) inherits(s, "RmbSpectrum2"))))
- if(!childrenSpectraOK) return("MS2 spectra are not of class RmbSpectrum2")
- return(TRUE)
- }
);
-setClass("RmbSpectrum2",
- representation = representation(
- satellite="logical",
- low="logical",
- rawOK ="logical",
- good = "logical",
- mzCalc = "numeric",
- formula = "numeric",
- dppm = "numeric"
- ),
- contains=c("Spectrum2"),
- prototype = prototype(
- satellite = logical(),
- low = logical(),
- rawOK = logical(),
- good = logical(),
- mzCalc = numeric(),
- formula = numeric(),
- dppm = numeric()
- ),
-)
+.RmbSpectraSetList <- setClass("RmbSpectraSetList", contains="SimpleList",
+ prototype=prototype(elementType="RmbSpectraSet"))
+
+
+
setGeneric("getData", function(s) standardGeneric("getData"))
setGeneric("setData", function(s, df) standardGeneric("setData"))
diff --git a/R/SpectrumMethods.R b/R/SpectrumMethods.R
index b139f38..ba480b3 100644
--- a/R/SpectrumMethods.R
+++ b/R/SpectrumMethods.R
@@ -6,7 +6,7 @@
setMethod("getData", c("RmbSpectrum2"), function(s)
{
peaks <- s@peaksCount
- cols <- c("mz", "intensity", "satellite", "low", "rawOK", "good", "mzCalc", "formula", "dppm")
+ cols <- c("mz", "intensity", "satellite", "low", "rawOK", "good", "mzCalc", "formula", "dbe", "formulaCount", "dppm", "dppmBest")
cols.isFilled <- unlist(lapply(cols, function(col) length(slot(s, col)) == peaks))
cols.filled <- cols[cols.isFilled]
df <- do.call(data.frame, lapply(cols.filled, function(col) slot(s, col)))
--
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