diff --git a/DESCRIPTION b/DESCRIPTION
index 11f273698fc94253f1925577ff4fad25235171c3..342da0989857ca8fc8f3ba413192e6f1572ef308 100755
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -49,9 +49,10 @@ Collate:
'SpectrumMethods.R'
'RmbWorkspace.R'
'RmbWorkspaceUpdate.R'
+ 'SpectraSetMethods.R'
+ 'AggregateMethods.R'
'validateMassBank.R'
- 'zzz.R'
'tools.R'
'msmsRead.R'
-
+ 'zzz.R'
\ No newline at end of file
diff --git a/NAMESPACE b/NAMESPACE
index 45a2b984e5fe6ec2214e2559d0fc12757189e154..08d541d588b58b4b7877847932df2baad6183d5e 100755
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,8 +1,8 @@
-# Generated by roxygen2 (4.1.1): do not edit by hand
+# Generated by roxygen2 (4.1.0): do not edit by hand
+S3method(c,msmsWSspecs)
export(CTS.externalIdSubset)
export(CTS.externalIdTypes)
-export(gatherPubChem)
export(RmbDefaultSettings)
export(RmbSettingsTemplate)
export(add.formula)
@@ -15,6 +15,7 @@ export(analyzeMsMs.formula)
export(analyzeMsMs.intensity)
export(annotator.default)
export(archiveResults)
+export(checkSpectra)
export(cleanElnoise)
export(combineMultiplicities)
export(compileRecord)
@@ -49,6 +50,8 @@ export(flatten)
export(formulastring.to.list)
export(gatherCompound)
export(gatherData)
+export(gatherDataBabel)
+export(gatherPubChem)
export(gatherSpectrum)
export(getCactus)
export(getCtsKey)
@@ -93,7 +96,9 @@ export(recalibrateSingleSpec)
export(recalibrateSpectra)
export(resetInfolists)
export(resetList)
+export(selectSpectra)
export(smiles2mass)
+export(spectraCount)
export(to.limits.rcdk)
export(toMassbank)
export(toRMB)
@@ -101,10 +106,14 @@ export(updateSettings)
export(validate)
exportClasses(mbWorkspace)
exportClasses(msmsWorkspace)
+exportMethods(checkSpectra)
+exportMethods(selectSpectra)
exportMethods(show)
+exportMethods(spectraCount)
import(Biobase)
import(MSnbase)
import(RCurl)
+import(Rcpp)
import(S4Vectors)
import(XML)
import(methods)
diff --git a/R/AggregateMethods.R b/R/AggregateMethods.R
new file mode 100644
index 0000000000000000000000000000000000000000..f6a845d9ddbb7a59b67268cc05e0da048f64ce11
--- /dev/null
+++ b/R/AggregateMethods.R
@@ -0,0 +1,24 @@
+
+#' @export
+setGeneric("peaksMatched", function(o) standardGeneric("peaksMatched"))
+
+#' @export
+setMethod("peaksMatched", c("data.frame"), function(o)
+ {
+ o[o$good,,drop=FALSE]
+ })
+
+#' @export
+setMethod("peaksMatched", c("msmsWorkspace"), function(o) peaksMatched(o@aggregated))
+
+#' @export
+setGeneric("peaksUnmatched", function(o) standardGeneric("peaksUnmatched"))
+
+#' @export
+setMethod("peaksUnmatched", c("data.frame"), function(o)
+ {
+ o[!o$good,,drop=FALSE]
+ })
+
+#' @export
+setMethod("peaksUnmatched", c("msmsWorkspace"), function(o) peaksUnmatched(o@aggregated))
\ No newline at end of file
diff --git a/R/RmbWorkspace.R b/R/RmbWorkspace.R
index 13b504bd56334dec89dc8e6d51db179935f292e3..3cdcdfccff9976fba355607be13c2eec171ccebb 100755
--- a/R/RmbWorkspace.R
+++ b/R/RmbWorkspace.R
@@ -62,9 +62,11 @@ setClassUnion("msmsWorkspaceOrNULL", "NULL")
representation = representation(
files = "character",
spectra = "RmbSpectraSetList",
+ aggregated = "data.frame",
parent = "msmsWorkspaceOrNULL",
analyzedSpecs = "list",
aggregatedSpecs = "list",
+
rc = "ANY",
rc.ms1 = "ANY",
recalibratedSpecs = "list",
diff --git a/R/RmbWorkspaceUpdate.R b/R/RmbWorkspaceUpdate.R
index df02a646b96bef27bd89b5385ef552f2d6a93bf6..0a700f77a7b8c2067e4669beffa6408a85f3e326 100644
--- a/R/RmbWorkspaceUpdate.R
+++ b/R/RmbWorkspaceUpdate.R
@@ -42,6 +42,7 @@
w.new@parent <- w.parent.new
}
w.new@spectra <- .updateObject.spectra(w.old@specs, w.old@analyzedSpecs)
+ w.new@aggregatedSpecs <- w.old@aggregatedSpecs
}
return(w.new)
@@ -63,58 +64,60 @@
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")
-
+ if(set@found)
+ {
+ 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$childHeaders, 1, function(line)
+ {
+ new("RmbSpectrum2",
+ precScanNum = as.integer(line["precursorScanNum"]),
+ precursorMz = line["precursorMZ"],
+ precursorIntensity = line["precursorIntensity"],
+ precursorCharge = as.integer(line["precursorCharge"]),
+ collisionEnergy = line["collisionEnergy"],
+ tic = line["totIonCurrent"],
+ rt = line["retentionTime"],
+ acquisitionNum = as.integer(line["acquisitionNum"]),
+ centroided = TRUE
+ )
+ })
+ # merge MSMS RmbSpectrum2 with header RmbSpectrum2
+ children <- mapply(function(c1,c2)
+ {
+ c2slots <- c("precScanNum","precursorMz", "precursorIntensity", "precursorCharge", "collisionEnergy",
+ "tic", "rt", "acquisitionNum", "centroided")
+ for(c2slot in c2slots)
+ slot(c1, c2slot) <- slot(c2, c2slot)
+ return(c1)
+ }, children.p1, children.p2)
+ set@children <- as(children, "SimpleList")
+ }
return(set)
})
spectra <- mapply(function(set, name)
@@ -132,107 +135,176 @@
{
if(length(analyzedSpec$msmsdata) != length(set@children))
stop("updateObject: Could not update object because data is inconsistent. length(analyzedSpec$msmsdata) != length(set@children)")
+
+ set@complete <- FALSE
+ set@empty <- FALSE
+
+
+ if(length(analyzedSpec$msmsdata) == 0)
+ {
+ empty <- TRUE
+ return(set)
+ }
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
+ if(msmsrecord$specOK)
+
+ spectrum@ok <- TRUE
+ else
+ spectrum@ok <- FALSE
# check if the spectrum has recalibrated masses; if yes, use those
if("mzRecal" %in% colnames(msmsrecord$childRaw))
mzcol <- "mzRecal"
else
mzcol <- "mz"
- spectrum@mz <- c(msmsrecord$childFilt$mzFound,
+
+ # create potentially missing data frames
+ if(!is.data.frame(msmsrecord$childFilt))
+ {
+ msmsrecord$childFilt <- data.frame()
+ msmsrecord$childRawLow[,"mzFound"] <- numeric()
+ msmsrecord$childRawLow[,"int"] <- numeric()
+ }
+ if(!is.data.frame(msmsrecord$childBad))
+ {
+ msmsrecord$childBad <- data.frame()
+ msmsrecord$childBad[,"mzFound"] <- numeric()
+ msmsrecord$childBad[,"int"] <- numeric()
+ }
+ if(!is.data.frame(msmsrecord$childUnmatched))
+ {
+ msmsrecord$childUnmatched <- data.frame()
+ msmsrecord$childUnmatched[,"mzFound"] <- numeric()
+ msmsrecord$childUnmatched[,"int"] <- numeric()
+ }
+ if(!is.data.frame(msmsrecord$childRawLow))
+ {
+ msmsrecord$childRawLow <- data.frame()
+ msmsrecord$childRawLow[,mzcol] <- numeric()
+ msmsrecord$childRawLow[,"int"] <- numeric()
+ }
+ if(!is.data.frame(msmsrecord$childRawSatellite))
+ {
+ msmsrecord$childRawSatellite <- data.frame()
+ msmsrecord$childRawSatellite[,mzcol] <- numeric()
+ msmsrecord$childRawSatellite[,"int"] <- numeric()
+
+ }
+ # note: mz/intensity are replaced with the values from the analyzed spectrum,
+ # such as to have a mass multiple times for multiple matched formulas
+
+ 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$childRawSatellite)))
- )
+ if(length(mz) > 0)
+ {
+ spectrum@mz <- mz
+ spectrum@intensity <- c(msmsrecord$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)))
+ )
+ }
+ else
+ {
+ # mz and intensity are already there
+ spectrum@satellite <- as.logical(rep(NA, spectrum@peaksCount))
+ spectrum@low <- as.logical(rep(NA, spectrum@peaksCount))
+ spectrum@rawOK <- as.logical(rep(FALSE, spectrum@peaksCount))
+ spectrum@good <- as.logical(rep(FALSE, spectrum@peaksCount))
+ spectrum@mzCalc <- as.numeric(rep(NA, spectrum@peaksCount))
+ spectrum@formula <- as.character(rep(NA, spectrum@peaksCount))
+ spectrum@dbe <- as.numeric(rep(NA, spectrum@peaksCount))
+ spectrum@formulaCount <- as.integer(rep(NA, spectrum@peaksCount))
+ spectrum@dppm <- as.numeric(rep(NA, spectrum@peaksCount))
+ spectrum@dppmBest <- as.numeric(rep(NA, spectrum@peaksCount))
+
+
+
+ }
- 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(
@@ -252,6 +324,14 @@
},
set@children, analyzedSpec$msmsdata)
set@children <- as(children, "SimpleList")
+
+ ok <- unlist(lapply(set@children, function(c) c@ok))
+ if(all(ok))
+ set@complete <- TRUE
+ if(all(!ok))
+ set@empty <- TRUE
+
+
set@mode <- analyzedSpec$mode
return(set)
},
@@ -263,6 +343,11 @@
}
+## .updateObject.aggregated <- function(aggregatedSpecs)
+## {
+##
+## }
+
# 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)
diff --git a/R/SpectraSetMethods.R b/R/SpectraSetMethods.R
new file mode 100644
index 0000000000000000000000000000000000000000..ec740a1adc44bfc20f3b8123ff3e96ce20640b85
--- /dev/null
+++ b/R/SpectraSetMethods.R
@@ -0,0 +1,67 @@
+
+
+# Accessor methods for found, complete, empty
+# .checkSpectra <-
+#' @export
+setGeneric("checkSpectra", function(s, property) standardGeneric("checkSpectra"))
+
+# .checkSpectra.RmbSpectraSet <-
+#' @export
+setMethod("checkSpectra", c("RmbSpectraSet", "character"), function(s, property)
+ {
+ #stopifnot(value=="logical", "For single spectraSet, only TRUE/FALSE output is supported.")
+ fields <- c("found", "complete", "empty")
+ if(!(property %in% fields)) stop("Only found, complete, empty properties are allowed")
+ slot(s, property)
+ })
+
+
+# .selectSpectra <-
+#' @export
+setGeneric("selectSpectra", def = function(s, property, value="logical") standardGeneric("selectSpectra"),
+ signature = c("s", "property"))
+
+# .selectSpectra.RmbSpectraSetList <-
+#' @export
+setMethod("selectSpectra", c("RmbSpectraSetList", "character"), function(s, property, value="logical")
+ {
+ matches <- unlist(lapply(s, function(s) checkSpectra(s, property)))
+ if(value == "logical")
+ return(matches)
+ else if(value == "index")
+ return(which(matches))
+ else if(value == "object")
+ return(s[matches])
+ else if(value == "mismatch")
+ return(s[!matches])
+ })
+
+# .selectSpectra.msmsWorkspace <-
+#' @export
+setMethod("selectSpectra", c("msmsWorkspace", "character"), function(s, property, value="logical")
+ selectSpectra(s@spectra, property, value))
+
+# .spectraCount <-
+#' @export
+setGeneric("spectraCount", function(s) standardGeneric("spectraCount"))
+
+# .spectraCount.RmbSpectraSet <-
+#' @export
+setMethod("spectraCount", c("RmbSpectraSet"), function(s)
+ {
+ length(s@children)
+ })
+
+# .spectraCount.RmbSpectraSetList <-
+#' @export
+setMethod("spectraCount", c("RmbSpectraSetList"), function(s)
+ {
+ unlist(lapply(s, spectraCount))
+ })
+
+
+# .spectraCount.msmsWorkspace <-
+#' @export
+setMethod("spectraCount", c("msmsWorkspace"), function(s)
+ spectraCount(s@spectra))
+
diff --git a/R/SpectrumMethods.R b/R/SpectrumMethods.R
index 5e05ca859e55a15fa448e125c2d0281b5564a729..097e0af6b3708e65c64f920326ba4804f7e462a5 100644
--- a/R/SpectrumMethods.R
+++ b/R/SpectrumMethods.R
@@ -3,6 +3,7 @@
# Author: stravsmi
###############################################################################
+#' @export
setMethod("getData", c("RmbSpectrum2"), function(s)
{
peaks <- s@peaksCount
@@ -14,7 +15,7 @@ setMethod("getData", c("RmbSpectrum2"), function(s)
df
})
-
+#' @export
setMethod("setData", c("RmbSpectrum2", "data.frame"), function(s, df, clean = TRUE)
{
cols <- c("mz", "intensity", "satellite", "low", "rawOK", "good", "mzCalc", "formula", "dppm")