improve checking for value attribute in getPeaklist()

sneumann · Aug 23, 2017 · 53f38e3 · 53f38e3
1 parent 6bda0bd
commit 53f38e3
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Showing 3 changed files with 4 additions and 3 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: CAMERA
-Version: 1.33.1
+Version: 1.33.1.90
 Date: 2017-08-18
 Title: Collection of annotation related methods for mass spectrometry data 
 Author: Carsten Kuhl, Ralf Tautenhahn, Hendrik Treutler, Steffen Neumann {ckuhl|htreutle|sneumann}@ipb-halle.de, rtautenh@scripps.edu

diff --git a/R/xsAnnotate.R b/R/xsAnnotate.R
@@ -1262,7 +1262,7 @@ getpspectra <- function(object, grp=NULL){
 setGeneric("getPeaklist", function(object, intval="into") standardGeneric("getPeaklist"))
 setMethod("getPeaklist", "xsAnnotate", function(object, intval="into") {
 
-  if (!sum(intval == c("into","intb","maxo", "intf", "maxf"))){
+  if (! intval %in% colnames(peaks(object(xcmsSet)))) {
        stop("unknown intensity value!")
   }
 

diff --git a/man/getPeaklist-methods.Rd b/man/getPeaklist-methods.Rd
@@ -11,7 +11,8 @@
 }
 \arguments{
   \item{object}{ xsAnnotate object}
-  \item{intval}{ Choose intensity values. Allowed values are into, maxo, intb, intf, maxf}
+  \item{intval}{ Choose intensity values. Allowed values are into, maxo, intb, intf,
+maxf, area, depending on the feature detection algorithm used.}
 }
 \details{
   This function extract the peaktable from an xsAnnotate object, containing three additional columns (isotopes, adducts, pseudospectrum) with represents the annotation results. For a grouped xcmsSet it returns the grouped peaktable.