From e0ef1f29d6fa8b1abc87fcd978e3a0c08aa51e44 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Sun, 17 May 2020 08:05:15 +0200
Subject: [PATCH] resources: ADDUCTMAP: change to the RChemMass list of adducts
* resources.R(ADDUCTMAP): Updated.
---
R/resources.R | 15 +++++++++------
1 file changed, 9 insertions(+), 6 deletions(-)
diff --git a/R/resources.R b/R/resources.R
index 885661a..1d60368 100644
--- a/R/resources.R
+++ b/R/resources.R
@@ -33,12 +33,15 @@ FN_LOC_SETID <-"setid.csv"
FN_COMP_TAB<-"comprehensive.csv"
FN_SPEC<-"specdata.rds"
FN_CONF <- "conf-state.yaml"
-ADDUCTMAP<-list("[M+H]+"="MpHp_mass",
- "[M-H]-"="MmHm_mass",
- "[M+NH4]+"="MpNH4_mass",
- "[M+Na]+"="MpNa_mass")
-
-DISP_ADDUCTMAP <- c(list("UNSET"="UNSET_ADDUCT_ERROR"),ADDUCTMAP)
+ADDUCTMAP <- RChemMass:::adducts$Name
+names(ADDUCTMAP) <- apply(RChemMass:::adducts,1,function(row) {
+ nm <- row[["Name"]]
+ sgn <- row[["Charge"]]
+ suff <- if (sgn > 0) "+" else if (sgn < 0) "-" else ""
+ paste0("[",nm,"]",suff)
+})
+
+DISP_ADDUCTMAP <- c(c("UNSET"="UNSET_ADDUCT_ERROR"),ADDUCTMAP)
TAG_NA <- "::UNSET::"
SET_NA <- "::UNSET::"
TAG_DEF <- TAG_NA
--
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