- make output of examples shorter

R/calculateCurveFit.R

@@ -18,7 +18,7 @@
 #' data(Blank2022intmat)
 #' 
 #' # for faster runtime we let it run on 5 peaks only
-#' calculateCurveFit(Blank2022intmat, idx = 1:5)
+#' fits <- calculateCurveFit(Blank2022intmat, idx = 1:5)
 calculateCurveFit <- function(intmat, idx, ...) {
   if (length(rownames(intmat)) == 0) {
     stop("intmat must have concentrations as rownames!\n")

R/calculatePeakstatistics.R

@@ -14,7 +14,10 @@
 #' data(Blank2022intmat)
 #' fits <- calculateCurveFit(Blank2022intmat, idx = 1:5)
 #' 
-#' calculatePeakStatistics(curveFits = fits, singlePeaks = Blank2022peaks, spec = Blank2022spec)
+#' peakstats <- calculatePeakStatistics(curveFits = fits, 
+#'                                      singlePeaks = Blank2022peaks, 
+#'                                      spec = Blank2022spec)
+#' head(peakstats)
 
 calculatePeakStatistics <- function(curveFits, singlePeaks, spec) {
   if (!is.list(curveFits)) {

R/extractIntensity.R

@@ -14,10 +14,11 @@
 #' data(Blank2022peaks)
 #' data(Blank2022spec)
 #' 
-#' extractIntensity(mz = c(409, 423, 440), 
-#'                  peaks = Blank2022peaks, 
-#'                  spec = Blank2022spec, 
-#'                  tol = 0.2)
+#' int <- extractIntensity(mz = c(409, 423, 440), 
+#'                         peaks = Blank2022peaks, 
+#'                         spec = Blank2022spec, 
+#'                         tol = 0.2)
+#' head(int)
 extractIntensity <- function(mz, peaks, spec, tol) {
   if(!(length(peaks) == length(spec))) {
     stop("length of peaks and spec must match.\n")

R/extractSpots.R

@@ -7,7 +7,7 @@
 #' @export
 #' @examples
 #' data(Blank2022spec)
-#' extractSpots(Blank2022spec)
+#' head(extractSpots(Blank2022spec))
 extractSpots <- function(spec) {
   if(!isMassSpectrumList(spec)) {
     if(!isMassPeaksList(spec)) {

R/getters.R

@@ -8,7 +8,7 @@
 #' @examples 
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
-#' getConc(Blank2022res)
+#' head(getConc(Blank2022res))
 
 getConc <- function(object) {
   stopIfNotIsMALDIassay(object)
@@ -45,7 +45,7 @@ getDirection <- function(model) {
 #' 
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
-#' getSingleSpecIntensity(Blank2022res, 2)
+#' head(getSingleSpecIntensity(Blank2022res, 2))
 getSingleSpecIntensity <- function(object, mz_idx) {
   s <- getSinglePeaks(object)
   mz <- mass(s[[1]]) # all single spectra have same mass axis
@@ -80,7 +80,7 @@ getSingleSpecIntensity <- function(object, mz_idx) {
 #' @examples
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
-#' getIntensityMatrix(Blank2022res, avg = TRUE, excludeNormMz = TRUE) 
+#' head(getIntensityMatrix(Blank2022res, avg = TRUE, excludeNormMz = TRUE) )
 getIntensityMatrix <- function(object, avg = FALSE, excludeNormMz =FALSE) {
 
   if(avg) {
@@ -159,7 +159,7 @@ getSNR <- function(object) {
 #' 
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
-#' getAvgSpectra(Blank2022res)
+#' getAvgSpectra(Blank2022res)[[1]]
 getAvgSpectra <- function(object) {
   stopIfNotIsMALDIassay(object)
   return(object@avgSpectra)
@@ -175,7 +175,7 @@ getAvgSpectra <- function(object) {
 #' @examples
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
-#' getAvgPeaks(Blank2022res)
+#' getAvgPeaks(Blank2022res)[[1]]
 getAvgPeaks <- function(object) {
   stopIfNotIsMALDIassay(object)
   return(object@avgPeaks)
@@ -191,7 +191,7 @@ getAvgPeaks <- function(object) {
 #' @examples
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
-#' getSinglePeaks(Blank2022res)
+#' getSinglePeaks(Blank2022res)[[1]]
 getSinglePeaks <- function(object) {
   stopIfNotIsMALDIassay(object)
   return(object@singlePeaks)
@@ -239,7 +239,7 @@ getVarFilterMethod <- function(object) {
 #' @examples
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
-#' getAppliedMzShift(Blank2022res)
+#' head(getAppliedMzShift(Blank2022res))
 getAppliedMzShift <- function(object) {
   stopIfNotIsMALDIassay(object)
   return(object@mzShifts)
@@ -255,7 +255,7 @@ getAppliedMzShift <- function(object) {
 #' @examples
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
-#' getAppliedNormFactors(Blank2022res)
+#' head(getAppliedNormFactors(Blank2022res))
 getAppliedNormFactors <- function(object) {
   stopIfNotIsMALDIassay(object)
   return(object@normFactors)
@@ -271,7 +271,7 @@ getAppliedNormFactors <- function(object) {
 #' @examples
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
-#' getCurveFits(Blank2022res)
+#' fits <- getCurveFits(Blank2022res)
 getCurveFits <- function(object) {
   stopIfNotIsMALDIassay(object)
   return(object@fits)
@@ -306,7 +306,7 @@ getDirectory <- function(object) {
 #' @examples
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
-#' getPeakStatistics(Blank2022res, summarise = TRUE)
+#' head(getPeakStatistics(Blank2022res, summarise = TRUE))
 getPeakStatistics <- function(object, summarise = FALSE) {
   stopIfNotIsMALDIassay(object)
   stats <- object@stats
@@ -400,7 +400,7 @@ getMzFromMzIdx <- function(object, mzIdx) {
 #' @examples
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
-#' getAllMz(Blank2022res)
+#' head(getAllMz(Blank2022res))
 getAllMz <- function(object, excludeNormMz = FALSE) {
   stopIfNotIsMALDIassay(object)
   if(!excludeNormMz) {
@@ -436,7 +436,10 @@ getAllMz <- function(object, excludeNormMz = FALSE) {
 #' @examples
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
+#' # spots per spectrum
 #' getSpots(Blank2022res, singleSpec = TRUE)
+#' 
+#' #spots per concentration
 #' getSpots(Blank2022res, singleSpec = FALSE)
 getSpots <- function(object, singleSpec = TRUE) {
   stopIfNotIsMALDIassay(object)
@@ -461,7 +464,7 @@ getSpots <- function(object, singleSpec = TRUE) {
 #' @examples
 #' # see example for `fitCurve()` to see how this data was generated
 #' data(Blank2022res)
-#' getFittingParameters(Blank2022res, summarise = FALSE)
+#' head(getFittingParameters(Blank2022res, summarise = FALSE))
 getFittingParameters <- function(object, summarise = FALSE) {
   stopIfNotIsMALDIassay(object)
 

R/sdMassSpectrum.R

@@ -196,7 +196,7 @@ sdMassSpectraFun <- function(l, mergeMetaData = TRUE) {
 #' @examples
 #' data(Blank2022spec)
 #' 
-#' sdMassSpectrum(Blank2022spec, labels = names(Blank2022spec))
+#' sdMassSpectrum(Blank2022spec, labels = names(Blank2022spec))[[1]]
 
 sdMassSpectrum <- function(l, labels, ...) {