add N/C-term modifications; closes #47

lgatto · Jun 21, 2015 · 62a3301 · 62a3301
1 parent 48655ee
commit 62a3301
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Showing 4 changed files with 45 additions and 2 deletions.
diff --git a/NEWS b/NEWS
@@ -5,6 +5,8 @@ CHANGES IN VERSION 1.17.6
  o Change the meaning of calculateFragments' "modifications" argument. Now the
    modification is added to the mass of the amino acid/peptide. Before it was
    replaced. <2015-06-21 Sun>
+ o calculateFragments gains the feature to handle N-/C-terminal modifications,
+   see #47. <2015-06-21 Sun>
 
 CHANGES IN VERSION 1.17.5
 -------------------------

diff --git a/R/functions-fragments.R b/R/functions-fragments.R
@@ -113,7 +113,7 @@
   if (neutralLoss) {
     df <- .neutralLoss(df)
   }
-  df
+  .terminalModifications(df, modifications=modifications)
 }
 
 #' adds neutral loss to data.frame generated by .calculateFragments
@@ -159,3 +159,22 @@
   df
 }
 
+#' adds nterm/cterm modifications to data.frame generated by .calculateFragments
+#' should be used after .neutralLoss
+#' @param df data.frame generated by. calculateFragments
+#' @return modified data.frame
+#' @noRd
+.terminalModifications <- function(df, modifications) {
+  affected <- c(Nterm="^[abc]_?$", Cterm="^[xyz]\\*?$")
+
+  for (term in c("Nterm", "Cterm")) {
+    if (term %in% names(modifications)) {
+      isAffected <- grep(affected[term], df$type)
+      if (length(isAffected)) {
+        df$mz[isAffected] <- df$mz[isAffected] + modifications[term]
+      }
+    }
+  }
+
+  df
+}
diff --git a/man/calculateFragments-methods.Rd b/man/calculateFragments-methods.Rd
@@ -28,7 +28,9 @@
     name must correspond to the one-letter-code of the modified amino acid and
     the \code{numeric} value must represent the mass that should be added to the
     original amino accid mass, default:
-    Carbamidomethyl \code{modifications=c(C=57.02146)}. }
+    Carbamidomethyl \code{modifications=c(C=57.02146)}. Use \code{Nterm} or
+    \code{Cterm} as names for modifications that should be added to the amino
+    respectively carboxyl-terminus.}
   \item{neutralLoss}{ \code{logical} if \code{TRUE} (default) neutral loss is
     also calculated. Currently water and ammonia loss (shown with an \code{_}
     respectively a \code{*} in the results). }
@@ -83,6 +85,9 @@ 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)
 

diff --git a/tests/testthat/test_fragments.R b/tests/testthat/test_fragments.R
@@ -63,6 +63,23 @@ test_that("calculateFragments", {
                calculateFragments("PQR", verbose=FALSE),
                check.attributes=FALSE, tolerance=1e-5)
 
+  ## neutral loss + nterm mod, rownames always differ
+  tpqr <- pqr[c(4:6, 13:15, 19:24),]
+  tpqr$mz[1:3] <- tpqr$mz[1:3]+229
+  expect_equal(tpqr,
+               calculateFragments("PQR", modifications=c(C=57.02146, Nterm=229),
+                                                         verbose=FALSE),
+               check.attributes=FALSE, tolerance=1e-5)
+
+  ## neutral loss + nterm + cterm mod, rownames always differ
+  tpqr$mz[c(4:6, 11:12)] <- tpqr$mz[c(4:6, 11:12)]-100
+  expect_equal(tpqr,
+               calculateFragments("PQR", modifications=c(C=57.02146,
+                                                         Nterm=229,
+                                                         Cterm=-100),
+                                                         verbose=FALSE),
+               check.attributes=FALSE, tolerance=1e-5)
+
   expect_equal(ace,
                calculateFragments("ACE", type=c("a", "b", "c", "x", "y", "z"),
                                   z=2, neutralLoss=FALSE, verbose=FALSE),