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Refactoring for xcmsEIC and xcmsFragments done.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,53 @@ | ||
| ## Methods for xcmsEIC | ||
| #' @include functions-xcmsEIC.R | ||
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| ############################################################ | ||
| ## show | ||
| setMethod("show", "xcmsEIC", function(object) { | ||
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| cat("An \"xcmsEIC\" object with", length(object@eic), "samples\n\n") | ||
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| cat("Time range: ", paste(round(range(object@rtrange), 1), collapse = "-"), | ||
| " seconds (", paste(round(range(object@rtrange)/60, 1), collapse = "-"), | ||
| " minutes)\n", sep = "") | ||
| cat("Mass range:", paste(round(range(object@mzrange, na.rm = TRUE), 4), collapse = "-"), | ||
| "m/z\n") | ||
| cat("EICs per sample:", nrow(object@mzrange), "\n") | ||
| cat("Retention times:", object@rt, "\n") | ||
| cat("xcmsSet group names: ") | ||
| if (length(object@groupnames)) | ||
| cat("present") | ||
| else | ||
| cat("absent") | ||
| cat("\n\n") | ||
| memsize <- object.size(object) | ||
| cat("Memory usage:", signif(memsize/2^20, 3), "MB\n") | ||
| }) | ||
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| ############################################################ | ||
| ## groupnames | ||
| setMethod("groupnames", "xcmsEIC", function(object) { | ||
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| object@groupnames | ||
| }) | ||
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| ############################################################ | ||
| ## sampnames | ||
| setMethod("sampnames", "xcmsEIC", function(object) { | ||
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| names(object@eic) | ||
| }) | ||
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| ############################################################ | ||
| ## mzrange | ||
| setMethod("mzrange", "xcmsEIC", function(object) { | ||
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| object@mzrange | ||
| }) | ||
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| ############################################################ | ||
| ## rtrange | ||
| setMethod("rtrange", "xcmsEIC", function(object) { | ||
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| object@rtrange | ||
| }) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| ## Methods for xcmsFragments. | ||
| #' @include functions-xcmsFragments.R | ||
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| ############################################################ | ||
| ## show | ||
| setMethod("show", "xcmsFragments", .xcmsFragments.show) | ||
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| ############################################################ | ||
| ## collect | ||
| setMethod("collect", "xcmsFragments", .xcmsFragments.collect) | ||
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| ############################################################ | ||
| ## plotTree | ||
| setMethod("plotTree", "xcmsFragments", .xcmsFragments.plotTree) | ||
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| ############################################################ | ||
| ## hasMSn | ||
| setMethod("hasMSn", "xcmsFragments", .xcmsFragments.hasMSn) | ||
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| ############################################################ | ||
| ## findneutral | ||
| setMethod("findneutral", "xcmsFragments", function(object, find, ppmE=25, print=TRUE) { | ||
| find<-range(ppmDev(Mr=find, ppmE)) | ||
| spectra<-unique(object@peaks[,"MSnParentPeakID"]) | ||
| found<-matrix(ncol=10) | ||
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| for (i in 1:length(spectra)){ | ||
| if(spectra[i] > 0){ | ||
| losses<-diff(sort(object@peaks[object@peaks[,"MSnParentPeakID"] ==spectra[i],"mz"] )) | ||
| if(length(losses) > 0){ | ||
| if(length(which(losses > find[1] & losses < find[2])) > 0){ | ||
| idx<-which(object@peaks[,"MSnParentPeakID"] == spectra[i]) | ||
| PrecursorMZ<-object@peaks[object@peaks[idx,"MSnParentPeakID"],"mz"] | ||
| CE<-object@peaks[object@peaks[idx,"MSnParentPeakID"],"CollisionEnergy"] | ||
| dat<-object@peaks[idx,c("MSnParentPeakID", "msLevel", "rt", "mz", | ||
| "intensity", "Sample", "GroupPeakMSn")] | ||
| found<-rbind(found, cbind(NeutralLoss=c(losses,0), PrecursorMz=PrecursorMZ, | ||
| dat[order(dat[,"mz"]),], CollisionEnergy=CE)) | ||
| } | ||
| } | ||
| } | ||
| } | ||
| if(nrow(found) >1){ | ||
| found<-found[2:nrow(found),] | ||
| } else{ | ||
| cat("Nothing found\n") | ||
| return(0) | ||
| } | ||
| if (print == TRUE){ | ||
| cat("We looked for", find[2], " to", find[1], "and found:\n") | ||
| print(found) | ||
| } | ||
| return(found) | ||
| }) | ||
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| ############################################################ | ||
| ## findMZ | ||
| setMethod("findMZ", "xcmsFragments", function(object, find, ppmE=25, print=TRUE) { | ||
| find<-range(ppmDev(Mr=find, ppmE)) | ||
| fragMZ<-0 | ||
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| found<- which(object@peaks[,"mz"] > find[1] & object@peaks[,"mz"] < find[2] & object@peaks[,"msLevel"] >1) | ||
| if(length(found) <1){ | ||
| cat("nothing was found\n") | ||
| return(0) | ||
| } | ||
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| PrecursorMZ<-object@peaks[object@peaks[found,"MSnParentPeakID"],"mz"] | ||
| CE<-object@peaks[object@peaks[found,"MSnParentPeakID"],"CollisionEnergy"] | ||
| foundFrag<-cbind(PrecursorMz=PrecursorMZ, object@peaks[found,c("MSnParentPeakID", "msLevel", | ||
| "rt", "mz", "intensity", "Sample", "GroupPeakMSn")], CollisionEnergy=CE) | ||
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| if (print == TRUE){ | ||
| cat("We looked for", find[2], " to", find[1], "and found:\n") | ||
| print(foundFrag) | ||
| } | ||
| return(foundFrag) | ||
| }) | ||
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