From 261786a33f1dc79125db4b89f282077d9e979104 Mon Sep 17 00:00:00 2001
From: ermueller <erik@east.de>
Date: Wed, 14 Oct 2015 01:15:22 +0200
Subject: [PATCH] FInish refactoring and adjusted other small things, 1 unit
test added
---
R/Isotopic_Annotation.R | 2 +-
R/leMsMs.r | 27 ++++++++++++++----
R/validateMassBank.R | 11 ++++++--
inst/unitTests/runit.DA.R | 2 +-
inst/unitTests/runit.EN_FC.R | 4 +--
inst/unitTests/runit.NOPEAKS.R | 9 ++++++
inst/validationTests/runit.MS2.test.R | 28 +++++++++----------
inst/validationTests/runit.MSn.test.slashes.R | 2 +-
8 files changed, 57 insertions(+), 28 deletions(-)
create mode 100644 inst/unitTests/runit.NOPEAKS.R
diff --git a/R/Isotopic_Annotation.R b/R/Isotopic_Annotation.R
index 3665e54..14aa8bb 100644
--- a/R/Isotopic_Annotation.R
+++ b/R/Isotopic_Annotation.R
@@ -8,7 +8,7 @@
#' @param conflict Either "isotopic"(Peak formulas are always chosen if they fit the requirements for an isotopic peak)
#' or "strict"(Peaks are only marked as isotopic when there hasn't been a formula assigned before.)
#' @param isolationWindow Half of the width of the isolation window in Da
-#' @param evalMode Currently no function yet, but planned
+#' @param evalMode Currently no function yet, but planned. Currently must be "complete"
#' @param plotSpectrum A boolean specifiying whether the spectrumshould be plotted
#' @param settings Options to be used for processing. Defaults to the options loaded via
#' \code{\link{loadRmbSettings}} et al. Refer to there for specific settings.
diff --git a/R/leMsMs.r b/R/leMsMs.r
index 6d2d850..ee59b2e 100755
--- a/R/leMsMs.r
+++ b/R/leMsMs.r
@@ -1104,8 +1104,12 @@ cleanElnoise <- function(peaks, noise=getOption("RMassBank")$electronicNoise,
problematicPeaks <- function(peaks_unmatched, peaks_matched, mode="pH")
{
# find spectrum maximum for each peak, and merge into table
- assIntMax <- as.data.frame(aggregate(peaks_matched$intensity,
+ if(nrow(peaks_matched) == 0){
+ assIntMax <- data.frame(list(integer(0),integer(0),integer(0)))
+ } else{
+ assIntMax <- as.data.frame(aggregate(peaks_matched$intensity,
by=list(peaks_matched$cpdID, peaks_matched$scan), max))
+ }
colnames(assIntMax) <- c("cpdID", "scan", "aMax")
peaks_unmatched <- merge(peaks_unmatched, assIntMax)
# which of these peaks are intense?
@@ -1818,8 +1822,12 @@ filterPeaksMultiplicity <- function(peaks, formulacol, recalcBest = TRUE)
if(!is.data.frame(peaks) || (nrow(peaks) == 0) )
{
- warning("filterPeaksMultiplicity: All peaks have been filtered.")
peaks <- cbind(peaks, data.frame(formulaMultiplicity=numeric()))
+ if(recalcBest){
+ warning("filterPeaksMultiplicity: All peaks have been filtered. The workflow can not be continued beyond this point.")
+ peaks$fM_factor <- as.factor(peaks$formulaMultiplicity)
+ return(peaks)
+ }
}
else
{
@@ -1960,7 +1968,7 @@ filterPeaksMultiplicity <- function(peaks, formulacol, recalcBest = TRUE)
#' @examples
#' \dontrun{
#' refilteredRcSpecs <- filterMultiplicity(
-#' reanalyzedRcSpecs, "myarchive", "pH")
+#' w, "myarchive", "pH")
#' }
#' @export
filterMultiplicity <- function(w, archivename=NA, mode="pH", recalcBest = TRUE,
@@ -1972,7 +1980,7 @@ filterMultiplicity <- function(w, archivename=NA, mode="pH", recalcBest = TRUE,
if(is.null(multiplicityFilter))
multiplicityFilter <- 2
- specs <- w@aggregated
+ specs <- w@aggregated
peaksFiltered <- filterPeaksMultiplicity(peaksMatched(specs),
"formula", recalcBest)
@@ -1998,7 +2006,11 @@ filterMultiplicity <- function(w, archivename=NA, mode="pH", recalcBest = TRUE,
specs <- addProperty(specs, "filterOK", "logical", FALSE)
- specs[specs$formulaMultiplicity > (multiplicityFilter - 1),"filterOK"] <- TRUE
+ OKindex <- which(specs$formulaMultiplicity > (multiplicityFilter - 1))
+
+ if(length(OKindex)){
+ specs[OKindex,"filterOK"] <- TRUE
+ }
peaksReanOK <- specs[
specs$filterOK & !is.na(specs$matchedReanalysis) & specs$matchedReanalysis,,drop=FALSE]
@@ -2009,7 +2021,10 @@ filterMultiplicity <- function(w, archivename=NA, mode="pH", recalcBest = TRUE,
peaksReanBad <- peaksReanOK[
!((peaksReanOK$mzFound < peaksReanOK$mzCenter - 1) |
(peaksReanOK$mzFound > peaksReanOK$mzCenter + 1)),]
- specs[match(peaksReanBad$index, specs$index),"filterOK"] <- FALSE
+ notOKindex <- match(peaksReanBad$index, specs$index)
+ if(length(notOKindex)){
+ specs[notOKindex,"filterOK"] <- FALSE
+ }
return(specs)
diff --git a/R/validateMassBank.R b/R/validateMassBank.R
index db1bd8a..f1aff63 100644
--- a/R/validateMassBank.R
+++ b/R/validateMassBank.R
@@ -19,8 +19,8 @@
#' @export
validate <- function(path, simple = TRUE) {
- requireNamespace("ontoCAT",quietly=TRUE)
- requireNamespace("RUnit",quietly=TRUE)
+ requireNamespace("ontoCAT",quietly=TRUE)
+ requireNamespace("RUnit",quietly=TRUE)
# Is the argument a directory?
# If yes, list the files
@@ -216,7 +216,12 @@ smiles2mass <- function(SMILES){
package="RMassBank"), testFileRegexp = "runit.DA.R",
#testFuncRegexp = "^test.+",
rngKind = "Marsaglia-Multicarry",
- rngNormalKind = "Kinderman-Ramage")
+ rngNormalKind = "Kinderman-Ramage")
+ testSuite3 <- RUnit::defineTestSuite("Evaluation of correct handling ig no peaks are found", dirs = system.file("unitTests",
+ package="RMassBank"), testFileRegexp = "runit.NOPEAKS.R",
+ #testFuncRegexp = "^test.+",
+ rngKind = "Marsaglia-Multicarry",
+ rngNormalKind = "Kinderman-Ramage")
testData <- suppressWarnings(RUnit::runTestSuite(testSuite))
testData2 <- suppressWarnings(RUnit::runTestSuite(testSuite2))
diff --git a/inst/unitTests/runit.DA.R b/inst/unitTests/runit.DA.R
index 8551904..afb5911 100644
--- a/inst/unitTests/runit.DA.R
+++ b/inst/unitTests/runit.DA.R
@@ -26,5 +26,5 @@ test.mzRRead <- function(){
}
}
- checkTrue(allOK)
+ RUnit::checkTrue(allOK)
}
\ No newline at end of file
diff --git a/inst/unitTests/runit.EN_FC.R b/inst/unitTests/runit.EN_FC.R
index 44ef280..f2e3ac4 100644
--- a/inst/unitTests/runit.EN_FC.R
+++ b/inst/unitTests/runit.EN_FC.R
@@ -1,10 +1,10 @@
test.eletronicnoise <- function(){
failpeaks <- read.csv("pH_narcotics_Failpeaks.csv")
- checkTrue(!any(apply(failpeaks,1,function(x) all(x[2:5] == c(1738,2819,668,201.69144)))))
+ RUnit::checkTrue(!any(apply(failpeaks,1,function(x) all(x[2:5] == c(1738,2819,668,201.69144)))))
}
test.formulacalculation <- function(){
failpeaks <- read.csv("pH_narcotics_Failpeaks.csv")
- checkTrue(!any(apply(failpeaks,1,function(x) all(x[2:5] == c(70,2758,321,56.04933)))))
+ RUnit::checkTrue(!any(apply(failpeaks,1,function(x) all(x[2:5] == c(70,2758,321,56.04933)))))
}
\ No newline at end of file
diff --git a/inst/unitTests/runit.NOPEAKS.R b/inst/unitTests/runit.NOPEAKS.R
new file mode 100644
index 0000000..06b2528
--- /dev/null
+++ b/inst/unitTests/runit.NOPEAKS.R
@@ -0,0 +1,9 @@
+test.nopeaks <- function(){
+ w <- newMsmsWorkspace()
+ w@aggregated <- data.frame(mzFound = numeric(0), intensity = numeric(0), good = logical(0), mzCalc = numeric(0), formula = character(0), dbe = numeric(0),
+ formulaCount = integer(0), dppm = numeric(0), dppmBest = numeric(0), scan = integer(0), cpdID = character(0), parentScan = integer(0), dppmRc = numeric(0),
+ index = integer(0), noise = logical(0), reanalyzed.formula = character(0), reanalyzed.mzCalc = numeric(0), reanalyzed.dppm = numeric(0),reanalyzed.formulaCount = numeric(0),
+ reanalyzed.dbe = numeric(0),matchedReanalysis = logical(0))
+ filterMultiplicity(w, mode="pH")
+ RUnit::checkTrue(TRUE)
+}
\ No newline at end of file
diff --git a/inst/validationTests/runit.MS2.test.R b/inst/validationTests/runit.MS2.test.R
index 8c4a5ee..8ea766f 100644
--- a/inst/validationTests/runit.MS2.test.R
+++ b/inst/validationTests/runit.MS2.test.R
@@ -1,34 +1,34 @@
test.NA <- function(){
- checkTrue(!(NA %in% as.matrix(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['PK$PEAK']])))
+ RUnit::checkTrue(!(NA %in% as.matrix(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['PK$PEAK']])))
}
test.peaksvsprecursor <- function(){
Max_Peak <- unname(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['PK$PEAK']][dim(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['PK$PEAK']])[1],1])
Precursor <- RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_M/Z']]
if(is.na(Precursor)){
- checkTrue(TRUE)
+ RUnit::checkTrue(TRUE)
}else{
- checkEquals(Max_Peak, Precursor, tolerance = Precursor/100)
+ RUnit::checkEquals(Max_Peak, Precursor, tolerance = Precursor/100)
}
}
test.precursormz <- function(){
precursorlist <- c("[M+H]+","[M+Na]+","[M-H]-","[M+HCOO-]-","[M]+","[M]-")
if(is.na(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_TYPE']]) || is.na(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_M/Z']])){
- checkTrue(TRUE)
+ RUnit::checkTrue(TRUE)
} else{
precursor <- grep(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_TYPE']],precursorlist, value = TRUE, fixed = TRUE)
if(precursor == "[M+H]+"){
- checkEquals(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_M/Z']],RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['CH$EXACT_MASS']] + 1.008,tolerance = 0.002)
+ RUnit::checkEquals(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_M/Z']],RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['CH$EXACT_MASS']] + 1.008,tolerance = 0.002)
}
if(precursor == "[M+Na]+"){
- checkEquals(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_M/Z']],RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['CH$EXACT_MASS']] + 22.989,tolerance = 0.002)
+ RUnit::checkEquals(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_M/Z']],RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['CH$EXACT_MASS']] + 22.989,tolerance = 0.002)
}
if(precursor == "[M-H]-"){
- checkEquals(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_M/Z']],RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['CH$EXACT_MASS']] - 1.008,tolerance = 0.002)
+ RUnit::checkEquals(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_M/Z']],RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['CH$EXACT_MASS']] - 1.008,tolerance = 0.002)
}
if(precursor == "[M+HCOO-]-"){
- checkEquals(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_M/Z']],RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['CH$EXACT_MASS']] + 45.017,tolerance = 0.002)
+ RUnit::checkEquals(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_M/Z']],RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['CH$EXACT_MASS']] + 45.017,tolerance = 0.002)
}
}
}
@@ -36,28 +36,28 @@ test.precursormz <- function(){
test.PrecursorType <- function(){
precursorlist <- c("[M+H]+","[M+Na]+","[M-H]-","[M+HCOO-]-","[M]+","[M]-")
if(is.na(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_TYPE']])){
- checkTrue(TRUE)
+ RUnit::checkTrue(TRUE)
}else{
- checkTrue(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_TYPE']] %in% precursorlist)
+ RUnit::checkTrue(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_TYPE']] %in% precursorlist)
}
}
test.smilesvsexactmass <- function(){
Mass_Calculated_Through_Smiles <- smiles2mass(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['CH$SMILES']])
Exact_Mass <- RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['CH$EXACT_MASS']]
- checkEquals(Mass_Calculated_Through_Smiles, Exact_Mass, tolerance = Exact_Mass/100)
+ RUnit::checkEquals(Mass_Calculated_Through_Smiles, Exact_Mass, tolerance = Exact_Mass/100)
}
test.sumintensities <- function(){
sumOfIntensities <- sum(RMassBank.env$mb[[RMassBank.env$testnumber]]@compiled_ok[[1]][['PK$PEAK']][,2])
- checkTrue(sumOfIntensities > 0)
+ RUnit::checkTrue(sumOfIntensities > 0)
}
test.TitleVsType <- function(){
RMassBank.env$testnumber <- RMassBank.env$testnumber + 1
if(is.na(RMassBank.env$mb[[RMassBank.env$testnumber-1]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_TYPE']])){
- checkTrue(TRUE)
+ RUnit::checkTrue(TRUE)
}else{
- checkTrue(grepl(RMassBank.env$mb[[RMassBank.env$testnumber-1]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_TYPE']], RMassBank.env$mb[[RMassBank.env$testnumber-1]]@compiled_ok[[1]][['RECORD_TITLE']], fixed = TRUE))
+ RUnit::checkTrue(grepl(RMassBank.env$mb[[RMassBank.env$testnumber-1]]@compiled_ok[[1]][['MS$FOCUSED_ION']][['PRECURSOR_TYPE']], RMassBank.env$mb[[RMassBank.env$testnumber-1]]@compiled_ok[[1]][['RECORD_TITLE']], fixed = TRUE))
}
}
diff --git a/inst/validationTests/runit.MSn.test.slashes.R b/inst/validationTests/runit.MSn.test.slashes.R
index 084c993..39912e2 100644
--- a/inst/validationTests/runit.MSn.test.slashes.R
+++ b/inst/validationTests/runit.MSn.test.slashes.R
@@ -1,5 +1,5 @@
test.slashes <- function(){
Type <- as.numeric(substring(mb@compiled_ok[[testNumber]][['AC$MASS_SPECTROMETRY']][['MS_TYPE']],first = 3))
slashes <- length(gregexpr('/', mb@compiled_ok[[testNumber]][['MS$FOCUSED_ION']][['PRECURSOR_M/Z']]))
- checkEquals(Type - 2,slashes)
+ RUnit::checkEquals(Type - 2,slashes)
}
\ No newline at end of file
--
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