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Export core function to identify isotopes #52

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Export core function to identify isotopes #52

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0392397
Export function to find isotopes based on mz and intensity values
jorainer Mar 20, 2020
7eb4602
Add unit test and restore old documentation
jorainer Mar 20, 2020
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6 changes: 3 additions & 3 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
Package: CAMERA
Version: 1.43.2
Version: 1.43.3
Date: 2020-02-10
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, [email protected]
Maintainer: Steffen Neumann <[email protected]>
Depends: R (>= 2.1.0), methods, Biobase, xcms (>= 1.13.5)
Imports: methods, xcms, RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph
Imports: RBGL, graph, graphics, grDevices, stats, utils, Hmisc, igraph
Suggests: faahKO, RUnit, BiocGenerics
Enhances: Rmpi, snow
Description: Annotation of peaklists generated by xcms, rule based annotation
Expand All @@ -16,4 +16,4 @@ ByteCompile: TRUE
URL: http://msbi.ipb-halle.de/msbi/CAMERA/
BugReports: https://github.com/sneumann/CAMERA/issues/new
biocViews: ImmunoOncology, MassSpectrometry, Metabolomics
RoxygenNote: 5.0.1
RoxygenNote: 7.1.0
9 changes: 8 additions & 1 deletion NAMESPACE
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Expand Up @@ -12,6 +12,11 @@ importFrom("grDevices", "rgb")
importFrom("stats", "cor.test")
importFrom("utils", "flush.console", "object.size", "read.table")
importFrom("igraph", "graph.data.frame", "label.propagation.community")
importFrom("graphics", "lines")
importFrom("grDevices", "rainbow")
importFrom("stats", "cutree", "density", "dist", "hclust", "median",
"na.omit", "prcomp", "pt")
importFrom("utils", "tail", "write.table")


importClassesFrom(Biobase, "Versioned")
Expand All @@ -31,7 +36,9 @@ export("annotate",
"xsAnnotate",
"compoundQuantiles",
"compoundLibraries",
"massWindowSizes")
"massWindowSizes",
"calcIsotopeMatrix",
"findIsotopePeaks")

exportClasses("xsAnnotate")
exportClasses("compoundQuantiles")
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4 changes: 2 additions & 2 deletions R/fct_findAdducts.R
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Expand Up @@ -76,13 +76,13 @@ annotateGrp <- function(ipeak, imz, rules, mzabs, devppm, isotopes, quasimolion,
return(NULL);
};

#Entferne Hypothesen, welche gegen OID-Score&Kausalität verstossen!
#Entferne Hypothesen, welche gegen OID-Score&Kausalitaet verstossen!
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Bonus points for translating german comments ...

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:) I leave that to you :) I just removed to german characters because devtools::document() failed crying for non-UTF8 encoding.

hypothese <- checkOidCausality(hypothese, rules[rules.idx, ]);
if(nrow(hypothese) < 2){
return(NULL);
};

#Prüfe IPS-Score
#Pruefe IPS-Score
hypothese <- checkIps(hypothese)
if(nrow(hypothese) < 2){
return(NULL)
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