more fixing

Author: lgatto

.github/workflows/check-bioc.yml

@@ -187,9 +187,10 @@ jobs:
           cd preprocessCore
           R CMD INSTALL --configure-args="--disable-threading"  .
 
-      - name: Install latest PSMatch from github
+      - name: Install latest PSMatch and PTMods from github
         run: |
           BiocManager::install("RforMassSpectrometry/PSMatch", ask = FALSE, force = TRUE)
+          BiocManager::install("RforMassSpectrometry/PTMods", ask = FALSE, force = TRUE)
         continue-on-error: true
         shell: Rscript {0}
 

DESCRIPTION

@@ -80,6 +80,7 @@ Depends:
 Imports:
     MsCoreUtils,
     PSMatch (>= 1.15.3),
+    PTMods (>= 0.99.5),
     BiocParallel,
     IRanges (>= 2.13.28),
     plyr,

NAMESPACE

@@ -21,6 +21,8 @@ importFrom(PSMatch,
            getAminoAcids,
            defaultNeutralLoss)
 
+importFrom(PTMods, convertAnnotation)
+
 importFrom(MsCoreUtils, closest, rbindFill,
            impute_matrix, normalize_matrix,
            robustSummary, medianPolish,

R/functions-Spectrum2.R

@@ -12,7 +12,6 @@
 calculateFragments_Spectrum2 <- function(sequence, object, tolerance=0.1,
                                          method=c("highest", "closest", "all"),
                                          relative=FALSE, ...) {
-
   isValidSequence <- !missing(sequence) && !is.na(sequence) &&
                      nchar(sequence)
   isValidSpectrum <- is(object, "Spectrum2") && peaksCount(object)

R/plotting-Spectrum.R

@@ -121,13 +121,13 @@ plotSpectrumVsSpectrum <- function(spectra, tolerance=25e-6,
                                 modifications = c(C = 57.02146),
                                 neutralLoss = defaultNeutralLoss(),
                                 z = 1,
-                                fragments = calculateFragments_Spectrum2(object,
-                                  sequence = sequence, tolerance = tolerance,
-                                  relative = relative, type = type, z = z,
-                                  fixed_modifications = modifications,
-                                  neutralLoss = neutralLoss,
-                                  verbose = isMSnbaseVerbose()) |>
-                               suppressWarnings(),
+                                fragments = suppressWarnings(
+                                    calculateFragments_Spectrum2(object,
+                                    sequence = sequence, tolerance = tolerance,
+                                    relative = relative, type = type, z = z,
+                                    fixed_modifications = modifications,
+                                    neutralLoss = neutralLoss,
+                                    verbose = isMSnbaseVerbose())),
                                fragments.cex = 0.75, peaks.lwd = 1, peaks.cex = 0.5, ...) {
   if (peaksCount(object) > 0 && !centroided(object)) {
     message("Your spectrum is not centroided.")

man/calculateFragments-methods.Rd

@@ -86,7 +86,7 @@
 \examples{
 ## find path to a mzXML file
 file <- dir(system.file(package = "MSnbase", dir = "extdata"),
-            full.name = TRUE, pattern = "mzXML$")
+            full.names = TRUE, pattern = "mzXML$")
 
 ## create basic MSnExp
 msexp <- readMSData(file, centroided = FALSE)
@@ -95,13 +95,7 @@ msexp <- readMSData(file, centroided = FALSE)
 msexp <- pickPeaks(msexp)
 
 ## calculate fragments for ACE with default modification
-calculateFragments("ACE", modifications=c(C=57.02146))
-
-## calculate fragments for ACE with an addition N-terminal modification
-calculateFragments("ACE", modifications=c(C=57.02146, Nterm=229.1629))
-
-## calculate fragments for ACE without any modifications
-calculateFragments("ACE", modifications=NULL)
+calculateFragments("ACE")
 
 calculateFragments("VESITARHGEVLQLRPK",
                    type=c("a", "b", "c", "x", "y", "z"),