use PSMatch fragment functions - close #574

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MSnbase
 Title: Base Functions and Classes for Mass Spectrometry and Proteomics
-Version: 2.29.1
+Version: 2.29.2
 Description: MSnbase provides infrastructure for manipulation,
              processing and visualisation of mass spectrometry and
              proteomics data, ranging from raw to quantitative and
@@ -79,6 +79,7 @@ Depends:
     ProtGenerics (>= 1.29.1)
 Imports:
     MsCoreUtils,
+    PSMatch,
     BiocParallel,
     IRanges (>= 2.13.28),
     plyr,
@@ -167,7 +168,6 @@ Collate:
     'functions-Spectrum1.R'
     'functions-Spectrum2.R'
     'functions-addIdentificationData.R'
-    'functions-fragments.R'
     'functions-mzR.R'
     'functions-plotting.R'
     'header.R'

NAMESPACE

@@ -17,6 +17,10 @@ import(scales)
 import(lattice)
 import(methods)
 
+importFrom(PSMatch,
+           getAminoAcids,
+           defaultNeutralLoss)
+
 importFrom(MsCoreUtils, closest, rbindFill,
            impute_matrix, normalize_matrix,
            robustSummary, medianPolish,
@@ -74,7 +78,6 @@ S3method(t, MSnSet)
 export(MSnSet,
        abstract,
        compareMSnSets,
-       defaultNeutralLoss,
        readMgfData,
        readMSData,
        readMSData2,
@@ -111,8 +114,6 @@ export(MSnSet,
        updateFeatureNames,
        updateSampleNames,
        normalise, ## for normalize method
-       get.amino.acids,
-       get.atomic.mass,
        listOf,
        npcv,
        selectFeatureData,
@@ -327,11 +328,11 @@ exportMethods(updateObject,
               "isolationWindowUpperMz",
               "filterPrecursorMz",
               "filterIsolationWindow",
-	      "alignRt",
-	      "filterIntensity",
-	      c,
-	      compareChromatograms,
-	      transformIntensity
+              "alignRt",
+              "filterIntensity",
+              c,
+              compareChromatograms,
+              transformIntensity
               )
 
 ## methods NOT exported

NEWS.md

@@ -1,5 +1,10 @@
 # MSnbase 2.29
 
+## MSnbase 2.29.2
+
+- Use fragmentation functions from PSMatch.
+- Mention R for Mass Spectrometry in start-up message.
+
 ## MSnbase 2.29.1
 
 - Check for identical ion header in `readMgfData()` (see [issue

R/environment.R

@@ -14,63 +14,4 @@ ClassVersions <- c(
 
 assign("ClassVersions", ClassVersions, envir = .MSnbaseEnv)
 
-assign("amino.acids",
-       data.frame(AA = c("peg","A","R","N","D","C","E",
-                    "Q","G","H","I","L", "K","M","F",
-                    "P","S","T","W","Y","V"),
-                  ResidueMass = c(44.00000,
-                    71.03711,  156.10111, 114.04293, 115.02694,
-                    103.00919, 129.04259, 128.05858, 57.02146,
-                    137.05891, 113.08406, 113.08406, 128.09496,
-                    131.04049, 147.06841, 97.05276,  87.03203,
-                    101.04768, 186.07931, 163.06333, 99.06841),
-                  Abbrev3 = c(NA,
-                    "Ala", "Arg", "Asn", "Asp", "Cys",
-                    "Glu", "Gln", "Gly", "His", "Ile",
-                    "Leu", "Lys", "Met", "Phe", "Pro",
-                    "Ser", "Thr", "Trp", "Tyr", "Val"),
-                  ImmoniumIonMass = c(NA,
-                    44.05003,  129.11400, 87.05584,  88.03986,  76.02210,
-                    102.05550, 101.07150, 30.03438,  110.07180, 86.09698,
-                    86.09698,  101.10790, 104.05340, 120.08130, 70.06568,
-                    60.04494,  74.06059,  159.09220, 136.07620, 72.08133),
-                  Name = c("Polyethylene glycol",
-                    "Alanine",    "Arginine",      "Asparagine", "Aspartic acid",
-                    "Cysteine",   "Glutamic acid", "Glutamine",  "Glycine",
-                    "Histidine",  "Isoleucine",    "Leucine",    "Lysine",
-                    "Methionine", "Phenylalanine", "Proline",    "Serine",
-                    "Threonine",  "Tryptophan",    "Tyrosine",   "Valine"),
-                  ## The hydrophobicity values are from JACS, 1962, 84: 4240-4246. (C. Tanford)
-                  Hydrophobicity = c(NA, 0.62, -2.53, -0.78, -0.9, 0.29,
-                    -0.74, -0.85, 0.48, -0.4, 1.38, 1.06, -1.5, 0.64, 1.19,
-                    0.12, -0.18, -0.05, 0.81, 0.26, 1.08),
-                  ## The hydrophilicity values are from PNAS, 1981, 78:3824-3828 (T.P.Hopp & K.R.Woods)
-                  Hydrophilicity = c(NA, -0.5, 3, 0.2, 3, -1, 3, 0.2, 0,
-                    -0.5, -1.8, -1.8, 3, -1.3, -2.5, 0, 0.3, -0.4, -3.4,
-                    -2.3, -1.5),
-                  SideChainMass = c(NA, 15, 101, 58, 59, 47, 73, 72,
-                    1, 82, 57, 57, 73, 75, 91, 42, 31, 45, 130, 107, 43),
-                  ## CRC Handbook of Chemistry and Physics, 66th ed., CRC Press, Boca Raton, Florida (1985).
-                  ## R.M.C. Dawson, D.C. Elliott, W.H. Elliott, K.M. Jones, Data for Biochemical Research 3rd ed., Clarendon Press Oxford
-                  pK1 = c(NA, 2.35, 2.18, 2.18, 1.88, 1.71, 2.19,
-                    2.17, 2.34, 1.78, 2.32, 2.36, 2.2, 2.28, 2.58,
-                    1.99, 2.21, 2.15, 2.38, 2.2, 2.29),
-                  pK2 = c(NA, 9.87, 9.09, 9.09, 9.6, 10.78, 9.67, 9.13,
-                    9.6, 8.97, 9.76, 9.6, 8.9, 9.21, 9.24, 10.6, 9.15,
-                    9.12, 9.39, 9.11, 9.74),
-                  pI = c(NA, 6.11, 10.76, 10.76, 2.98, 5.02, 3.08,
-                    5.65, 6.06, 7.64, 6.04, 6.04, 9.47, 5.74, 5.91,
-                    6.3, 5.68, 5.6, 5.88, 5.63, 6.02)),
-       envir = .MSnbaseEnv)
-
-assign("atomic.mass",
-          ## taken from:
-          ## http://www.chem.ualberta.ca/~massspec/atomic_mass_abund.pdf
-          c(H=1.007825,
-            C=12,
-            N=14.003074,
-            O=15.994915,
-            p=1.007276),
-       envir = .MSnbaseEnv)
-
 lockEnvironment(.MSnbaseEnv,bindings=TRUE)

R/functions-Spectrum2.R

@@ -7,7 +7,7 @@
 #' equal
 #' @param method matching method
 #' @param relative relative (or absolute) deviation
-#' @param ... further arguments passed to calculateFragments
+#' @param ... further arguments passed to `PSMarch:::.calculateFragments()`
 #' @noRd
 calculateFragments_Spectrum2 <- function(sequence, object, tolerance=0.1,
                                          method=c("highest", "closest", "all"),

R/functions-mzR.R

@@ -76,14 +76,14 @@ plotMzDelta_list <- function(object,            ## peakLists
                         ggtitle("Histogram of Mass Delta Distribution")
     if (withLabels) {
         y_offset <- x_offset <- rep(0.5, 21)
-        names(y_offset) <- names(x_offset) <- .get.amino.acids()$AA
+        names(y_offset) <- names(x_offset) <- PSMatch::getAminoAcids()$AA
         x_offset[c("I", "L", "K", "Q")] <- 1
         y_offset[c("V", "C")] <- 1
         y_offset[c("P", "T")] <- 0
         y_offset[c("N", "E")] <- 1
         y_offset[c("K", "Q", "I", "L")] <- 0
         y_offset[c("D", "M")] <- 0
-        aa <- cbind(.get.amino.acids(), x_offset, y_offset)
+        aa <- cbind(PSMatch::getAminoAcids(), x_offset, y_offset)
         ## removing Isoleucine, as it has the same residue mass
         ## as leucine, and updating leucine's label to I/L
         aa$AA <- as.character(aa$AA)

R/methods-fragments.R

@@ -3,7 +3,7 @@ setMethod("calculateFragments", c("character", "missing"),
                    modifications = c(C = 57.02146),
                    neutralLoss = defaultNeutralLoss(),
                    verbose = isMSnbaseVerbose()) {
-            l <- lapply(sequence, .calculateFragments,
+            l <- lapply(sequence, PSMatch:::.calculateFragments,
                         type = type, z = z, modifications = modifications,
                         neutralLoss = neutralLoss, verbose = verbose)
             return(do.call(rbind, l))