remove can email

R/functions-MSnSet.R

@@ -114,8 +114,8 @@ updateFeatureNames <- function(object, label, sep = ".") {
 ##' @return A \code{matrix} of dimensions
 ##'     \code{length(levels(factor(fData(object)[, fcol])))} by
 ##'     \code{ncol(object)} of integers.
-##' @author Laurent Gatto <lg390@@cam.ac.uk>, Sebastian Gibb
-##'     <mail@@sebastiangibb.de>
+##' @author Laurent Gatto and Sebastian Gibb
+##'
 ##' @examples
 ##' data(msnset)
 ##' n <- 2

man/FeatComp-class.Rd

@@ -60,7 +60,7 @@
     \item{\code{all}:}{Object of class \code{"logical"} defining if all
       features of only a subset were compared. One expects that
       \code{name == "all"} when \code{all} is \code{TRUE}. }
-    
+
   }
 }
 
@@ -73,8 +73,8 @@
   \describe{
 
     \item{compfnames}{\code{signature(x = "MSnSet", y = "MSnSet", fcol1
-	= "character", fcol2 = "character", simplify = "logical",
-	verbose = "logical")}: creates the \code{FeatComp} comparison
+        = "character", fcol2 = "character", simplify = "logical",
+        verbose = "logical")}: creates the \code{FeatComp} comparison
       object for instances \code{x} and \code{y}. The feature
       variables to be considered to details feature comparison can be
       defined by \code{fcol1} (default is \code{"markers"} and
@@ -91,15 +91,15 @@
       \code{x}. Additional parameters \code{fcol1}, \code{fcol2},
       \code{simplify} and \code{verbose} are passed to the pairwise
       comparison method. }
-    
+
     \item{show}{\code{signature(object = "FeatComp")}: prints a summary
       of the \code{object}. }
 
   }
 }
 
 \author{
-  Laurent Gatto <lg390@cam.ac.uk> and Thomas Naake
+  Laurent Gatto and Thomas Naake
 }
 
 \seealso{

man/FeaturesOfInterest-class.Rd

@@ -61,9 +61,9 @@
 
 
 \section{Objects from the Class}{
-  
+
   Objects can be created with the respective \code{FeaturesOfInterest}
-  and \code{FoICollection} constructors. 
+  and \code{FoICollection} constructors.
 
   \code{FeaturesOfInterest} instances can be generated in two different
   ways: the constructor takes either (1) a set of features names (a
@@ -86,8 +86,8 @@
   \code{FoICollection} instances can be constructed by creating an empty
   collection and serial additions of \code{FeaturesOfInterest} using
   \code{addFeaturesOfInterest} or by passing a list of
-  \code{FeaturesOfInterest} instance. 
-  
+  \code{FeaturesOfInterest} instance.
+
 }
 
 \section{Slots}{
@@ -141,29 +141,29 @@
 
     \item{description}{\code{signature(object = "FeaturesOfInterest")}:
       returns the description of \code{object}. }
-    
+
     \item{foi}{\code{signature(object = "FeaturesOfInterest")}: returns
       the features of interests. }
-    
+
     \item{length}{\code{signature(x = "FeaturesOfInterest")}: returns
       the number of features of interest in \code{x}. }
 
     \item{show}{\code{signature(object = "FeaturesOfInterest")}:
       displays \code{object}. }
 
     \item{fnamesIn}{\code{signature(x = "FeaturesOfInterst", y =
-	"MSnSet", count = "logical")}: if \code{count} is \code{FALSE}
-	(default), return a logical indicating whether there is at least
-	one feautre of interest present in \code{x}? Otherwise, returns
-	the number of such features. Works also with matrices and
-	data.frames. }
+        "MSnSet", count = "logical")}: if \code{count} is \code{FALSE}
+        (default), return a logical indicating whether there is at least
+        one feautre of interest present in \code{x}? Otherwise, returns
+        the number of such features. Works also with matrices and
+        data.frames. }
 
     \item{[}{Subsetting works like lists. Returns a new
       \code{FoICollection}.}
-    
+
     \item{[[}{Subsetting works like lists. Returns a new
-      \code{FeatureOfInterest}.}         
-    
+      \code{FeatureOfInterest}.}
+
   }
 
   \code{FoICollection} class:
@@ -184,25 +184,25 @@
       in the collection \code{x}. }
 
     \item{addFeaturesOfInterest}{\code{signature(x =
-	"FeaturesOfInterest", y = "FoICollection")}: add the
-	\code{FeaturesOfInterest} instance \code{x} to
-	\code{FoICollection} \code{y}. If \code{x} is already present, a
-	message is printed and \code{y} is returned unchanged. }
+        "FeaturesOfInterest", y = "FoICollection")}: add the
+        \code{FeaturesOfInterest} instance \code{x} to
+        \code{FoICollection} \code{y}. If \code{x} is already present, a
+        message is printed and \code{y} is returned unchanged. }
 
     \item{rmFeaturesOfInterest}{\code{signature(object =
-	"FoICollection", i = "numeric")}: removes the \code{i}th
+        "FoICollection", i = "numeric")}: removes the \code{i}th
       \code{FeatureOfInterest} in the collection \code{object}. }
 
     \item{show}{\code{signature(object = "FoICollection")}: displays
       \code{object}. }
 
   }
 }
-  
+
 
 
 \author{
-  Laurent Gatto <lg390@cam.ac.uk>
+  Laurent Gatto
 }
 
 
@@ -257,4 +257,3 @@ rmFeaturesOfInterest(xx, 1)
 }
 
 \keyword{classes}
-

man/MIAPE-class.Rd

@@ -48,7 +48,7 @@
 
 \description{
   The Minimum Information About a Proteomics Experiment.
-  The current implementation is based on the MIAPE-MS 2.4 document. 
+  The current implementation is based on the MIAPE-MS 2.4 document.
 }
 
 \section{Slots}{
@@ -73,14 +73,14 @@
       standard 'YYYY-MM-DD' format (with hyphens). }
     \item{\code{name}:}{Object of class \code{character} containing the
       name of the (stable) primary contact person for this data set;
-      this could be the experimenter, lab head, line manager, \ldots}  
+      this could be the experimenter, lab head, line manager, \ldots}
     \item{\code{lab}:}{Object of class \code{character} containing the
       laboratory where the experiment was conducted. }
     \item{\code{contact}:}{Object of class \code{character} containing
       contact information for lab and/or experimenter. }
     \item{\code{email}:}{Object of class \code{character} containing
       tmail contact information for the primary contact person (see
-      \code{name} above). } 
+      \code{name} above). }
     \item{\code{instrumentModel}:}{Object of class \code{character}
       indicating the model of the mass spectrometer used to generate the
       data. }
@@ -135,7 +135,7 @@
       way of accessing this data. }
     \item{\code{detectorType}:}{Object of class \code{character}
       describing the type of detector used in the machine (microchannel
-      plate, channeltron, \ldots). }  
+      plate, channeltron, \ldots). }
     \item{\code{detectorSensitivity}:}{Object of class \code{character}
       giving and appropriate measure of the sensitivity of the described
       detector (e.g. applied voltage). }
@@ -149,18 +149,18 @@
     \item{\code{abstract(MIAPE)}:}{An accessor function for
       \code{abstract}. }
     \item{\code{expinfo(MIAPE)}:}{An accessor function for \code{name},
-      \code{lab}, \code{contact}, \code{title}, and \code{url}.} 
+      \code{lab}, \code{contact}, \code{title}, and \code{url}.}
     \item{\code{notes(MIAPE), notes(MIAPE) <- value}:}{Accessor
-      functions for \code{other}. \code{notes(MIAME) <- character} 
+      functions for \code{other}. \code{notes(MIAME) <- character}
       \emph{appends} character to notes; use \code{notes(MIAPE) <- list}
-      to replace the notes entirely.} 
+      to replace the notes entirely.}
     \item{\code{otherInfo(MIAPE)}:}{An accessor function for
-      \code{other}.} 
+      \code{other}.}
     \item{\code{preproc(MIAPE)}:}{An accessor function for
-      \code{preprocessing}.} 
+      \code{preprocessing}.}
     \item{\code{pubMedIds(MIAPE), pubMedIds(MIAME) <- value}:}{Accessor
-      function for \code{pubMedIds}.} 
-    \item{\code{expemail(MIAPE)}:}{An accessor function for 
+      function for \code{pubMedIds}.}
+    \item{\code{expemail(MIAPE)}:}{An accessor function for
       \code{email} slot.}
     \item{\code{exptitle(MIAPE)}:}{An accessor function for
       \code{title} slot.}
@@ -185,14 +185,14 @@
       \code{MIAME} class. Used when converting an \code{MSnSet} into an
       \code{ExpressionSet}. }
   }
-  
+
   MIAPE-specific methods, including MIAPE-MS meta-data:
   \describe{
     \item{\code{show(MIAPE)}:}{Displays the experiment data.}
     \item{\code{msInfo(MIAPE)}:}{Displays 'MIAPE-MS' information.}
   }
 }
-  
+
 \section{Extends}{
   Class \code{"\linkS4class{MIAxE}"}, directly.
   Class \code{"\linkS4class{Versioned}"}, by class "MIAxE", distance 2.
@@ -201,10 +201,10 @@
 \references{
   About MIAPE: \url{http://www.psidev.info/index.php?q=node/91}, and
   references therein, especially 'Guidelines for reporting the use of mass
-  spectrometry in proteomics', Nature Biotechnology 26, 860-861 (2008).  
+  spectrometry in proteomics', Nature Biotechnology 26, 860-861 (2008).
 }
 \author{
-  Laurent Gatto <lg390@cam.ac.uk>
+  Laurent Gatto
 }
 
 % \note{

man/MSmap-class.Rd

@@ -39,34 +39,34 @@
 \section{Objects from the Class}{
   Objects can be created with the \code{MSmap} constructor. The
   constructor has the following arguments:
-  
+
   \describe{
 
     \item{object}{An object created by \code{mzR::openMSfile} or an
       instance of class \code{\linkS4class{OnDiskMSnExp}}. If the latter
       contains data from multiple files, a warning will be issued and
       the first one will be used. }
-      
+
     \item{lowMz}{A \code{numeric} of length 1 defining the lower bound
       of the M/Z range of the MS map.}
 
     \item{highMz}{A \code{numeric} of length 1 defining the upper bound
       of the M/Z range of the MS map. }
 
     \item{resMz}{The resolution along the M/Z range. }
-    
+
     \item{hd}{An optional \code{data.frame} as produced by
       \code{mzR::header(object)}. If missing, will be computer within
       the function. Ignored when \code{object} is an
       \code{OnDiskMSnExp}.}
-    
+
     \item{zeroIsNA}{Set 0 intensities to \code{NA}. This can be used
       to clarify the 3 dimensional plot produce by \code{plot3D}.}
   }
 }
 
 
-\section{Slots}{  
+\section{Slots}{
   \describe{
     \item{\code{call}:}{Object of class \code{"call"} - the call used to
       generate the instance. }
@@ -79,7 +79,7 @@
     \item{\code{rt}:}{Object of class \code{"numeric"} with the
       retention times of the map spectra. }
     \item{\code{ms}:}{Object of class \code{"numeric"} with the MS
-      levels of the spectra. }    
+      levels of the spectra. }
     \item{\code{t}:}{Object of class \code{"logical"} indicating if the
     instance has been transposed. }
     \item{\code{filename}:}{Object of class \code{"character"}
@@ -93,15 +93,15 @@
       convert the \code{MSmap} instance in a \code{data.frame}. Useful
       for plotting with \code{lattice} or \code{ggplot2}. }
     \item{fileName}{\code{signature(object = "MSmap")}: returns the raw
-      data filename. } 
+      data filename. }
     \item{msLevel}{\code{signature(object = "MSmap")}: returns the MS
       level of the map spectra. }
     \item{msMap}{\code{signature(object = "MSmap")}: returns the actual
       map \code{matrix}. }
     \item{mz}{\code{signature(object = "MSmap", ...)}: returns the M/Z values
       of the map. Additional arguments are currently ignored. }
     \item{rtime}{\code{signature(object = "MSmap", ...)}: returns retention
-      time values of the map. Additional arguments are currently ignored.}	
+      time values of the map. Additional arguments are currently ignored.}
     \item{mzRes}{\code{signature(object = "MSmap")}: returns the
       resolution with which the sample along the M/Z range was done. }
     \item{dim}{\code{signature(x = "MSmap")}: returns the dimensions of
@@ -124,7 +124,7 @@
 }
 
 \author{
-  Laurent Gatto <lg390@cam.ac.uk>
+  Laurent Gatto
 }
 
 \examples{
@@ -137,7 +137,7 @@
     mzf <- pxget(px1, i)
 
     ## Using an mzRpwiz object
-    ## reads the data 
+    ## reads the data
     ms <- openMSfile(mzf)
     hd <- header(ms)
 
@@ -163,7 +163,7 @@
 
     ## Using an OnDiskMSnExp object and accessors
     msn <- readMSData(mzf, mode = "onDisk")
-    
+
     ## a set of spectra of interest: MS1 spectra eluted
     ## between 30 and 35 minutes retention time
     ms1 <- which(msLevel(msn) == 1)
@@ -178,7 +178,7 @@
     i <- ms1[which(rtsel)][1]
     j <- ms1[which(rtsel)][2]
     M4 <- MSmap(msn, i:j, 100, 1000, 1)
-    plot3D(M4)    
+    plot3D(M4)
 }
 }
 

man/MSnExp-class.Rd

@@ -349,15 +349,15 @@
     }
 
     \item{filterPrecursorMz}{\code{signature(object = "MSnExp", mz, ppm
-	= 10)}: retain spectra with a precursor m/z equal or similar to
-	the one defined with parameter \code{mz}. Parameter \code{ppm}
-	allows to define an accepted difference between the provided m/z
-	and the spectrum's m/z.
+        = 10)}: retain spectra with a precursor m/z equal or similar to
+        the one defined with parameter \code{mz}. Parameter \code{ppm}
+        allows to define an accepted difference between the provided m/z
+        and the spectrum's m/z.
     }
 
     \item{filterIsolationWindow}{\code{signature(object = "MSnExp",
-	mz)}: retain spectra with isolation windows that contain
-	(which m/z range contain) the specified m/z.
+        mz)}: retain spectra with isolation windows that contain
+        (which m/z range contain) the specified m/z.
     }
   }
 }
@@ -369,7 +369,7 @@
 }
 
 \author{
-  Laurent Gatto <lg390@cam.ac.uk>
+  Laurent Gatto
 }
 
 \seealso{