Merge pull request #61 from sneumann/master

Please pull improved show() method and roxygen generated manpages

R/RmbWorkspace.R

@@ -235,16 +235,35 @@ setMethod("show", "msmsWorkspace",
 			cat(" with files: \n")
 			sapply(basename(object@files), function(x) cat("  -", x, "\n"))
                         ## msmsWorkflow: Step 1. Get peaks ?
+						numspecs <- 0
                         dummy <- sapply(object@specs, function(x) cat(" -", x$id, "\t foundOK:", x$foundOK, "\n"))
                         cat("Peaks found:\n")
-                        dummy <- sapply(object@specs, function(x) cat(" -", x$id, "\t peaks:",
-                                                                      sapply(x$peaks, nrow), "\n"))
+						ids <- vector()
+                        dummy1 <- sapply(object@specs, function(x) {
+							cat(" -", x$id, "\t peaks:",
+                            sapply(x$peaks, nrow), "\n")
+							ids <<- c(ids, x$id)
+							numspecs <<- numspecs + 1
+							return(sapply(x$peaks, nrow))
+						})
 																	  
                         ## msmsWorkflow: Step 2. First analysis pre recalibration
                         cat("Peaks annotated after Step 2:\n")
-                        dummy <- sapply(object@analyzedSpecs, function(x) cat(" -", x$id, "\t peaks:",
-                                                                      sapply(x$msmsdata, function(x) length(unique(x$childFilt[,1]))), "\n"))
-                        
+                        dummy2 <- sapply(object@analyzedSpecs, function(x) {
+							cat(" -", x$id, "\t peaks:",
+                            sapply(x$msmsdata, function(x) length(unique(x$childFilt[,1]))), "\n")
+							return(sapply(x$msmsdata, function(x) length(unique(x$childFilt[,1]))))
+						})
+						
+						PeakMat <- matrix(dummy1-dummy2,numspecs,numspecs)
+						
+						tempids <- ids
+                        cat("Peaks without annotation:\n")
+						sapply(split(PeakMat, rep(1:nrow(PeakMat), each = ncol(PeakMat))), function(x){
+							cat(" -", tempids[1], "\t number of peaks filtered:", x, "\n")
+							tempids <<- tempids[-1]
+						})
+						
                         ## msmsWorkflow: Step 3. Aggregate all spectra
 						cat("Peaks aggregated after Step 3:\n")
 						cat("Matched Peaks:\n")
@@ -273,12 +292,29 @@ setMethod("show", "msmsWorkspace",
 						cat("Peaks found after Step 4:\n")
 						dummy <- sapply(object@recalibratedSpecs, function(x) cat(" -", x$id, "\t foundOK:", x$foundOK, "\n"))
                         cat("Peaks found:\n")
-                        dummy <- sapply(object@recalibratedSpecs, function(x) cat(" -", x$id, "\t peaks:",
-                                                                      sapply(x$peaks, nrow), "\n"))
+                        dummy4 <- sapply(object@recalibratedSpecs, function(x){ 
+																	cat(" -", x$id, "\t peaks:",
+																		sapply(x$peaks, nrow), "\n")
+																		return(sapply(x$peaks, nrow))
+																	})
+						
                         ## msmsWorkflow: Step 5. Reanalyze recalibrated spectra
 						cat("Peaks found after Step 5:\n")
-                        dummy <- sapply(object@analyzedRcSpecs, function(x) cat(" -", x$id, "\t peaks:",
-                                                                      sapply(x$msmsdata, function(x) length(unique(x$childFilt[,1]))), "\n"))
+                        dummy5 <- sapply(object@analyzedRcSpecs, function(x){
+																	cat(" -", x$id, "\t peaks:",
+                                                                    sapply(x$msmsdata, function(x) length(unique(x$childFilt[,1]))), "\n")
+																	return(sapply(x$msmsdata, function(x) length(unique(x$childFilt[,1]))))
+																})
+																
+						PeakMat <- matrix(dummy4-dummy5,numspecs,numspecs)
+						
+						tempids <- ids
+                        cat("Peaks without annotation in reanalyzed recalibrated peaks:\n")
+						sapply(split(PeakMat, rep(1:nrow(PeakMat), each = ncol(PeakMat))), function(x){
+							cat(" -", tempids[1], "\t number of peaks filtered:", x, "\n")
+							tempids <<- tempids[-1]
+						})
+						
                         ## msmsWorkflow: Step 6. Aggregate recalibrated results
 						cat("Peaks found after Step 6:\n")
 						cat("Matched Peaks:\n")

man/findMsMsHRperxcms.direct.Rd

+\name{findMsMsHRperxcms.direct}
+\alias{findMsMsHRperxcms.direct}
+\title{Read in mz-files using XCMS}
+\usage{
+  findMsMsHRperxcms.direct(fileName, cpdID, mode = "pH",
+    findPeaksArgs = NULL, plots = FALSE, MSe = FALSE)
+}
+\arguments{
+  \item{fileName}{The path to the mz-file that should be
+  read}
+
+  \item{cpdID}{The compoundID of the compound that has been
+  used for the file}
+
+  \item{mode}{The ionization mode that has been used for
+  the spectrum represented by the peaklist}
+
+  \item{findPeaksArgs}{A list of arguments that will be
+  handed to the xcms-method findPeaks via do.call}
+
+  \item{plots}{A parameter that determines whether the
+  spectra should be plotted or not}
+
+  \item{MSe}{A boolean value that determines whether the
+  spectra were recorded using MSe or not}
+}
+\value{
+  The \code{msmsWorkspace} with the additional peaklist
+  added to the right spectrum
+}
+\description{
+  Picks peaks from mz-files and returns the pseudospectra
+  that CAMERA creates with the help of XCMS
+}
+\examples{
+\dontrun{
+		fileList <- list.files(system.file("XCMSinput", package = "RMassBank"), "Glucolesquerellin", full.names=TRUE)[3]
+		loadList(system.file("XCMSinput/compoundList.csv",package="RMassBank"))
+     psp <- findMsMsHRperxcms.direct(fileList,2184)
+}
+}
+\author{
+  Erik Mueller
+}
+\seealso{
+  \code{\link{msmsWorkflow}}
+}
+

man/plotMbWorkspaces.Rd

+\name{plotMbWorkspaces}
+\alias{plotMbWorkspaces}
+\title{Plots mbWorkspaces}
+\usage{
+  plotMbWorkspaces(w1, w2 = NULL)
+}
+\arguments{
+  \item{w1}{The \code{mbWorkspace} to be plotted}
+
+  \item{w2}{Another optional \code{mbWorkspace} be plotted
+  as a reference.}
+}
+\value{
+  A logical indicating whether the information was plotted
+  or not
+}
+\description{
+  Plots the peaks of one or two \code{mbWorkspace} to
+  compare them.
+}
+\details{
+  This functions plots one or two \code{mbWorkspace}s in
+  case the use has used different methods to acquire
+  similar spectra. \code{w1} must always be supplied, while
+  \code{w2} is optional. The wokspaces need to be fully
+  processed for this function to work.
+}
+\examples{
+#
+\dontrun{plotMbWorkspaces(w1,w2)}
+}
+\author{
+  Erik Mueller
+}
+

man/toRMB.Rd

+\name{toRMB}
+\alias{toRMB}
+\title{Conversion of XCMS-pseudospectra into RMassBank-spectra}
+\usage{
+  toRMB(msmsXCMSspecs, cpdID, mode, MS1spec)
+}
+\arguments{
+  \item{msmsXCMSspecs}{The compoundID of the compound that
+  has been used for the peaklist}
+
+  \item{cpdID}{The compound ID of the substance of the
+  given spectrum}
+
+  \item{mode}{The ionization mode that has been used for
+  the spectrum}
+
+  \item{MS1spec}{The MS1-spectrum from XCMS, which can be
+  optionally supplied}
+}
+\value{
+  One list element of the (at)specs-entry from an
+  msmsWorkspace
+}
+\description{
+  Converts a pseudospectrum extracted from XCMS using
+  CAMERA into the msmsWorkspace(at)specs-format that
+  RMassBank uses
+}
+\examples{
+\dontrun{
+		XCMSpspectra <- findmsmsHRperxcms.direct("Glucolesquerellin_2184_1.mzdata", 2184)
+     wspecs <- toRMB(XCMSpspectra)
+}
+}
+\author{
+  Erik Mueller
+}
+\seealso{
+  \code{\link{msmsWorkspace-class}}
+}
+